Starting phenix.real_space_refine on Wed May 28 06:09:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cku_45654/05_2025/9cku_45654.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cku_45654/05_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_45654/05_2025/9cku_45654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cku_45654/05_2025/9cku_45654.map" model { file = "/net/cci-nas-00/data/ceres_data/9cku_45654/05_2025/9cku_45654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cku_45654/05_2025/9cku_45654.cif" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.08, per 1000 atoms: 0.65 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: 7.89 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.41 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: 11.94 Time building geometry restraints manager: 9.44 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: 3.820 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: 0.590 Extract box with map and model: 1.210 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 70.100 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (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 TRP 0.010 0.002 TRP A 30 HIS 0.005 0.001 HIS E 87 PHE 0.016 0.002 PHE E 198 TYR 0.014 0.002 TYR G 34 ARG 0.015 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.10345 ( 860) hydrogen bonds : angle 5.81079 ( 2403) covalent geometry : bond 0.00445 (15415) covalent geometry : angle 0.67354 (20966) *********************** 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 : 2.465 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: 3.3194 time to fit residues: 864.0484 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 : 2.294 ------------------------------------------------------------------------------- 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 165 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 F 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112238 restraints weight = 53770.304| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.36 r_work: 0.3048 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 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 = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15415 Z= 0.214 Angle : 0.625 11.322 20966 Z= 0.346 Chirality : 0.067 1.377 2513 Planarity : 0.006 0.064 2728 Dihedral : 4.957 28.095 2163 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 1974 helix: 1.73 (0.17), residues: 746 sheet: 1.15 (0.25), residues: 372 loop : -0.28 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.013 0.001 HIS G 129 PHE 0.020 0.002 PHE E 198 TYR 0.019 0.003 TYR G 34 ARG 0.006 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.06044 ( 860) hydrogen bonds : angle 5.62694 ( 2403) covalent geometry : bond 0.00449 (15415) covalent geometry : angle 0.62533 (20966) *********************** 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 216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 207 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8201 (mtp) cc_final: 0.7813 (mtm) REVERT: A 21 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7800 (mmmm) REVERT: A 91 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7633 (tp30) REVERT: B 23 HIS cc_start: 0.7832 (m-70) cc_final: 0.7499 (m90) REVERT: B 87 HIS cc_start: 0.8532 (p90) cc_final: 0.7713 (m90) REVERT: B 260 ASN cc_start: 0.8416 (m-40) cc_final: 0.8173 (m110) REVERT: C 20 MET cc_start: 0.7939 (mtp) cc_final: 0.7501 (mmt) REVERT: C 29 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: C 87 HIS cc_start: 0.8418 (p90) cc_final: 0.7874 (m-70) REVERT: D 20 MET cc_start: 0.7717 (mtp) cc_final: 0.7110 (mpt) REVERT: D 87 HIS cc_start: 0.8418 (p90) cc_final: 0.7905 (m-70) REVERT: D 259 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7130 (mtt-85) REVERT: F 23 HIS cc_start: 0.7903 (m-70) cc_final: 0.7595 (m90) REVERT: F 53 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7747 (mp0) REVERT: F 144 LYS cc_start: 0.8399 (mttt) cc_final: 0.7969 (mtmt) REVERT: G 239 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7940 (tmt90) outliers start: 9 outliers final: 7 residues processed: 212 average time/residue: 3.4498 time to fit residues: 796.7512 Evaluate side-chains 212 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LYS 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 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 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 5 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 152 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- 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 H 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116624 restraints weight = 61226.898| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.42 r_work: 0.3059 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1069 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= 0.135 Angle : 0.529 11.122 20966 Z= 0.289 Chirality : 0.066 1.418 2513 Planarity : 0.004 0.041 2728 Dihedral : 4.600 26.777 2163 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.73 % Allowed : 7.65 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 1974 helix: 2.10 (0.18), residues: 746 sheet: 1.20 (0.25), residues: 372 loop : -0.21 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.008 0.001 HIS G 129 PHE 0.014 0.002 PHE E 198 TYR 0.011 0.002 TYR G 34 ARG 0.008 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 860) hydrogen bonds : angle 5.27147 ( 2403) covalent geometry : bond 0.00272 (15415) covalent geometry : angle 0.52901 (20966) *********************** 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 222 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8187 (mtp) cc_final: 0.7819 (mtm) REVERT: A 21 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7784 (mmmm) REVERT: A 91 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7614 (tp30) REVERT: B 23 HIS cc_start: 0.7790 (m-70) cc_final: 0.7454 (m90) REVERT: B 260 ASN cc_start: 0.8376 (m-40) cc_final: 0.8109 (m110) REVERT: C 20 MET cc_start: 0.7926 (mtp) cc_final: 0.7477 (mmt) REVERT: C 29 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: C 87 HIS cc_start: 0.8378 (p90) cc_final: 0.7864 (m-70) REVERT: D 20 MET cc_start: 0.7725 (mtp) cc_final: 0.7109 (mpt) REVERT: D 87 HIS cc_start: 0.8419 (p90) cc_final: 0.7886 (m90) REVERT: D 259 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7113 (mtt-85) REVERT: E 91 GLU cc_start: 0.7059 (mp0) cc_final: 0.6526 (pm20) REVERT: F 23 HIS cc_start: 0.7890 (m-70) cc_final: 0.7603 (m90) REVERT: F 53 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7734 (mp0) REVERT: F 144 LYS cc_start: 0.8397 (mttt) cc_final: 0.7964 (mtmt) outliers start: 11 outliers final: 4 residues processed: 216 average time/residue: 3.4075 time to fit residues: 800.9598 Evaluate side-chains 211 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 138 optimal weight: 0.0060 chunk 154 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 H 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115743 restraints weight = 59742.891| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.43 r_work: 0.3101 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15415 Z= 0.108 Angle : 0.492 11.127 20966 Z= 0.266 Chirality : 0.066 1.432 2513 Planarity : 0.004 0.046 2728 Dihedral : 4.336 25.591 2163 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.61 % Allowed : 8.26 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 1974 helix: 2.33 (0.18), residues: 746 sheet: 1.18 (0.25), residues: 372 loop : -0.10 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.003 0.001 HIS E 72 PHE 0.010 0.001 PHE E 198 TYR 0.010 0.001 TYR G 256 ARG 0.009 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 860) hydrogen bonds : angle 5.04219 ( 2403) covalent geometry : bond 0.00219 (15415) covalent geometry : angle 0.49240 (20966) *********************** 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 216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8179 (mtp) cc_final: 0.7808 (mtm) REVERT: A 21 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7797 (mmtm) REVERT: A 91 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7612 (tp30) REVERT: B 23 HIS cc_start: 0.7748 (m-70) cc_final: 0.7429 (m90) REVERT: B 260 ASN cc_start: 0.8358 (m-40) cc_final: 0.8102 (m110) REVERT: C 20 MET cc_start: 0.7929 (mtp) cc_final: 0.7470 (mmt) REVERT: C 29 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: C 87 HIS cc_start: 0.8320 (p90) cc_final: 0.7867 (m90) REVERT: C 259 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7406 (mtp85) REVERT: D 20 MET cc_start: 0.7743 (mtp) cc_final: 0.7125 (mpt) REVERT: D 87 HIS cc_start: 0.8415 (p90) cc_final: 0.7891 (m90) REVERT: D 259 ARG cc_start: 0.7596 (ttt90) cc_final: 0.7112 (mtt-85) REVERT: E 87 HIS cc_start: 0.8618 (p90) cc_final: 0.7996 (m90) REVERT: F 23 HIS cc_start: 0.7886 (m-70) cc_final: 0.7578 (m90) REVERT: F 144 LYS cc_start: 0.8378 (mttt) cc_final: 0.7967 (mtmt) REVERT: H 46 VAL cc_start: 0.7451 (t) cc_final: 0.7169 (p) outliers start: 8 outliers final: 4 residues processed: 211 average time/residue: 3.3748 time to fit residues: 775.0765 Evaluate side-chains 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 212 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 29 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 260 ASN B 87 HIS D 72 HIS D 104 ASN H 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111692 restraints weight = 59496.872| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.44 r_work: 0.3049 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 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 = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15415 Z= 0.184 Angle : 0.582 11.164 20966 Z= 0.321 Chirality : 0.066 1.410 2513 Planarity : 0.005 0.055 2728 Dihedral : 4.776 28.885 2163 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.92 % Allowed : 7.89 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 1974 helix: 1.95 (0.18), residues: 746 sheet: 1.13 (0.25), residues: 381 loop : -0.27 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 30 HIS 0.005 0.001 HIS E 87 PHE 0.018 0.002 PHE E 198 TYR 0.016 0.002 TYR G 34 ARG 0.008 0.001 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.05707 ( 860) hydrogen bonds : angle 5.45242 ( 2403) covalent geometry : bond 0.00382 (15415) covalent geometry : angle 0.58212 (20966) *********************** 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 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8171 (mtp) cc_final: 0.7796 (mtm) REVERT: A 21 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7792 (mmtm) REVERT: A 91 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7604 (tp30) REVERT: B 23 HIS cc_start: 0.7736 (m-70) cc_final: 0.7415 (m90) REVERT: B 106 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7482 (mptt) REVERT: B 260 ASN cc_start: 0.8383 (m-40) cc_final: 0.8120 (m110) REVERT: C 20 MET cc_start: 0.7936 (mtp) cc_final: 0.7483 (mmt) REVERT: C 29 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: C 87 HIS cc_start: 0.8409 (p90) cc_final: 0.7890 (m90) REVERT: C 179 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7740 (ptp-170) REVERT: D 20 MET cc_start: 0.7760 (mtp) cc_final: 0.7086 (mpt) REVERT: D 87 HIS cc_start: 0.8428 (p90) cc_final: 0.7884 (m-70) REVERT: D 259 ARG cc_start: 0.7616 (ttt90) cc_final: 0.7112 (mtt-85) REVERT: F 23 HIS cc_start: 0.7882 (m-70) cc_final: 0.7575 (m90) REVERT: F 53 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: F 144 LYS cc_start: 0.8405 (mttt) cc_final: 0.7976 (mtmt) outliers start: 13 outliers final: 7 residues processed: 211 average time/residue: 3.4935 time to fit residues: 800.4558 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 : 2.351 ------------------------------------------------------------------------------- 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 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 53 GLU 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 13 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS 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 = 0.3585 r_free = 0.3585 target = 0.140792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111952 restraints weight = 59186.252| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.44 r_work: 0.3053 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15415 Z= 0.177 Angle : 0.571 11.183 20966 Z= 0.314 Chirality : 0.066 1.408 2513 Planarity : 0.005 0.048 2728 Dihedral : 4.765 29.260 2163 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.98 % Allowed : 8.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 1974 helix: 1.91 (0.18), residues: 746 sheet: 1.15 (0.25), residues: 381 loop : -0.32 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.006 0.001 HIS B 87 PHE 0.019 0.002 PHE E 198 TYR 0.015 0.002 TYR G 34 ARG 0.011 0.001 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 860) hydrogen bonds : angle 5.42387 ( 2403) covalent geometry : bond 0.00368 (15415) covalent geometry : angle 0.57053 (20966) *********************** 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 222 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8159 (mtp) cc_final: 0.7779 (mtm) REVERT: A 21 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7778 (mmtm) REVERT: A 91 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7616 (tp30) REVERT: B 23 HIS cc_start: 0.7725 (m-70) cc_final: 0.7389 (m90) REVERT: B 260 ASN cc_start: 0.8386 (m-40) cc_final: 0.8122 (m110) REVERT: C 20 MET cc_start: 0.7924 (mtp) cc_final: 0.7476 (mmt) REVERT: C 29 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8267 (tm-30) REVERT: C 87 HIS cc_start: 0.8403 (p90) cc_final: 0.7886 (m90) REVERT: C 179 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7750 (ptp-170) REVERT: D 20 MET cc_start: 0.7772 (mtp) cc_final: 0.7102 (mpt) REVERT: D 87 HIS cc_start: 0.8416 (p90) cc_final: 0.7846 (m-70) REVERT: D 259 ARG cc_start: 0.7614 (ttt90) cc_final: 0.7112 (mtt-85) REVERT: F 23 HIS cc_start: 0.7838 (m-70) cc_final: 0.7542 (m90) REVERT: F 53 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: F 144 LYS cc_start: 0.8401 (mttt) cc_final: 0.7961 (mtmt) outliers start: 13 outliers final: 7 residues processed: 215 average time/residue: 3.4251 time to fit residues: 801.7961 Evaluate side-chains 216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 167 SER Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain G residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 130 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 87 HIS 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 = 0.3604 r_free = 0.3604 target = 0.142245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114113 restraints weight = 55998.189| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.39 r_work: 0.3072 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15415 Z= 0.139 Angle : 0.531 11.117 20966 Z= 0.290 Chirality : 0.066 1.414 2513 Planarity : 0.005 0.054 2728 Dihedral : 4.588 27.005 2163 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.92 % Allowed : 8.20 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 1974 helix: 2.10 (0.18), residues: 746 sheet: 1.18 (0.25), residues: 372 loop : -0.22 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.006 0.001 HIS B 87 PHE 0.015 0.002 PHE E 198 TYR 0.012 0.002 TYR G 34 ARG 0.011 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 860) hydrogen bonds : angle 5.23452 ( 2403) covalent geometry : bond 0.00286 (15415) covalent geometry : angle 0.53102 (20966) *********************** 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 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8101 (mtp) cc_final: 0.7730 (mtm) REVERT: A 21 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7784 (mmtm) REVERT: A 91 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7597 (tp30) REVERT: B 23 HIS cc_start: 0.7723 (m-70) cc_final: 0.7394 (m90) REVERT: B 260 ASN cc_start: 0.8374 (m-40) cc_final: 0.8113 (m110) REVERT: C 20 MET cc_start: 0.7915 (mtp) cc_final: 0.7482 (mmt) REVERT: C 29 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: C 87 HIS cc_start: 0.8353 (p90) cc_final: 0.7885 (m90) REVERT: C 179 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7750 (ptp-170) REVERT: D 20 MET cc_start: 0.7714 (mtp) cc_final: 0.7076 (mpt) REVERT: D 87 HIS cc_start: 0.8391 (p90) cc_final: 0.7855 (m90) REVERT: D 259 ARG cc_start: 0.7594 (ttt90) cc_final: 0.7122 (mtt-85) REVERT: F 23 HIS cc_start: 0.7863 (m-70) cc_final: 0.7575 (m90) REVERT: F 53 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: F 144 LYS cc_start: 0.8367 (mttt) cc_final: 0.7948 (mtmt) outliers start: 12 outliers final: 8 residues processed: 213 average time/residue: 3.4460 time to fit residues: 798.3583 Evaluate side-chains 216 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 2.535 ------------------------------------------------------------------------------- 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 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 182 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 193 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 87 HIS 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 = 0.3620 r_free = 0.3620 target = 0.143537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115342 restraints weight = 57426.122| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.41 r_work: 0.3096 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15415 Z= 0.115 Angle : 0.502 11.146 20966 Z= 0.272 Chirality : 0.065 1.424 2513 Planarity : 0.004 0.059 2728 Dihedral : 4.388 25.238 2163 Min Nonbonded Distance : 2.430 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 1974 helix: 2.29 (0.18), residues: 746 sheet: 1.17 (0.25), residues: 372 loop : -0.14 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 30 HIS 0.007 0.001 HIS B 87 PHE 0.011 0.001 PHE E 198 TYR 0.009 0.001 TYR G 256 ARG 0.012 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 860) hydrogen bonds : angle 5.07461 ( 2403) covalent geometry : bond 0.00235 (15415) covalent geometry : angle 0.50223 (20966) *********************** 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 219 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8109 (mtp) cc_final: 0.7739 (mtm) REVERT: A 21 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7793 (mmtm) REVERT: A 91 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7621 (tp30) REVERT: B 23 HIS cc_start: 0.7681 (m-70) cc_final: 0.7353 (m90) REVERT: B 260 ASN cc_start: 0.8364 (m-40) cc_final: 0.8122 (m110) REVERT: C 20 MET cc_start: 0.7906 (mtp) cc_final: 0.7461 (mmt) REVERT: C 29 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: C 87 HIS cc_start: 0.8334 (p90) cc_final: 0.7877 (m90) REVERT: D 20 MET cc_start: 0.7722 (mtp) cc_final: 0.7084 (mpt) REVERT: D 87 HIS cc_start: 0.8415 (p90) cc_final: 0.7866 (m90) REVERT: D 259 ARG cc_start: 0.7580 (ttt90) cc_final: 0.7101 (mtt-85) REVERT: E 87 HIS cc_start: 0.8635 (p90) cc_final: 0.8006 (m90) REVERT: F 23 HIS cc_start: 0.7856 (m-70) cc_final: 0.7574 (m90) REVERT: F 53 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: F 144 LYS cc_start: 0.8363 (mttt) cc_final: 0.7947 (mtmt) REVERT: G 417 GLN cc_start: 0.7982 (tp40) cc_final: 0.7669 (tp40) outliers start: 9 outliers final: 5 residues processed: 213 average time/residue: 3.4706 time to fit residues: 801.0271 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 : 2.165 ------------------------------------------------------------------------------- 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 F residue 53 GLU 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 1 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN B 87 HIS 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 = 0.3576 r_free = 0.3576 target = 0.140079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110703 restraints weight = 63765.353| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.65 r_work: 0.3023 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15415 Z= 0.213 Angle : 0.617 11.290 20966 Z= 0.340 Chirality : 0.066 1.396 2513 Planarity : 0.006 0.062 2728 Dihedral : 4.834 18.997 2161 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.04 % Allowed : 8.75 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 1974 helix: 1.83 (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 TRP 0.009 0.002 TRP A 30 HIS 0.009 0.001 HIS D 72 PHE 0.020 0.002 PHE E 198 TYR 0.019 0.003 TYR G 34 ARG 0.011 0.001 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.06013 ( 860) hydrogen bonds : angle 5.55476 ( 2403) covalent geometry : bond 0.00449 (15415) covalent geometry : angle 0.61679 (20966) *********************** 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 217 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8111 (mtp) cc_final: 0.7733 (mtm) REVERT: A 21 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7783 (mmtm) REVERT: A 91 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7607 (tp30) REVERT: B 23 HIS cc_start: 0.7709 (m-70) cc_final: 0.7360 (m90) REVERT: B 87 HIS cc_start: 0.8512 (p90) cc_final: 0.7706 (m-70) REVERT: B 260 ASN cc_start: 0.8443 (m-40) cc_final: 0.8187 (m110) REVERT: C 20 MET cc_start: 0.7915 (mtp) cc_final: 0.7444 (mmt) REVERT: C 29 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: C 87 HIS cc_start: 0.8426 (p90) cc_final: 0.7877 (m90) REVERT: C 179 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7779 (ptp-170) REVERT: D 20 MET cc_start: 0.7700 (mtp) cc_final: 0.7030 (mpt) REVERT: D 87 HIS cc_start: 0.8442 (p90) cc_final: 0.7864 (m-70) REVERT: D 259 ARG cc_start: 0.7601 (ttt90) cc_final: 0.7079 (mtt-85) REVERT: F 23 HIS cc_start: 0.7814 (m-70) cc_final: 0.7530 (m90) REVERT: F 53 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: F 144 LYS cc_start: 0.8369 (mttt) cc_final: 0.7915 (mtmt) outliers start: 14 outliers final: 7 residues processed: 207 average time/residue: 3.5521 time to fit residues: 797.4159 Evaluate side-chains 209 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 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 53 GLU 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 147 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.141367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113241 restraints weight = 54831.981| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.37 r_work: 0.3059 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15415 Z= 0.169 Angle : 0.567 11.138 20966 Z= 0.311 Chirality : 0.065 1.404 2513 Planarity : 0.005 0.075 2728 Dihedral : 4.719 18.558 2161 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.86 % Allowed : 8.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 1974 helix: 1.90 (0.18), residues: 746 sheet: 1.18 (0.25), residues: 372 loop : -0.30 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 30 HIS 0.004 0.001 HIS E 87 PHE 0.018 0.002 PHE E 198 TYR 0.015 0.002 TYR G 34 ARG 0.013 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 860) hydrogen bonds : angle 5.39701 ( 2403) covalent geometry : bond 0.00351 (15415) covalent geometry : angle 0.56655 (20966) ********************** 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 214 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 MET cc_start: 0.8118 (mtp) cc_final: 0.7748 (mtm) REVERT: A 21 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7803 (mmmm) REVERT: A 91 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7614 (tp30) REVERT: B 23 HIS cc_start: 0.7724 (m-70) cc_final: 0.7376 (m90) REVERT: B 87 HIS cc_start: 0.8528 (p90) cc_final: 0.7775 (m90) REVERT: B 260 ASN cc_start: 0.8378 (m-40) cc_final: 0.8132 (m110) REVERT: C 20 MET cc_start: 0.7924 (mtp) cc_final: 0.7488 (mmt) REVERT: C 29 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: C 87 HIS cc_start: 0.8395 (p90) cc_final: 0.7887 (m90) REVERT: C 179 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7765 (ptp-170) REVERT: D 20 MET cc_start: 0.7718 (mtp) cc_final: 0.7082 (mpt) REVERT: D 87 HIS cc_start: 0.8394 (p90) cc_final: 0.7823 (m-70) REVERT: D 259 ARG cc_start: 0.7602 (ttt90) cc_final: 0.7113 (mtt-85) REVERT: F 23 HIS cc_start: 0.7852 (m-70) cc_final: 0.7575 (m90) REVERT: F 53 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: F 144 LYS cc_start: 0.8369 (mttt) cc_final: 0.7958 (mtmt) outliers start: 11 outliers final: 6 residues processed: 206 average time/residue: 3.4082 time to fit residues: 761.9953 Evaluate side-chains 208 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 95 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.140098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111283 restraints weight = 60194.709| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.44 r_work: 0.3018 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15415 Z= 0.238 Angle : 0.645 11.536 20966 Z= 0.357 Chirality : 0.067 1.398 2513 Planarity : 0.006 0.094 2728 Dihedral : 4.928 19.645 2161 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.92 % Allowed : 8.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 1974 helix: 1.69 (0.18), residues: 746 sheet: 1.14 (0.25), residues: 381 loop : -0.40 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP A 30 HIS 0.007 0.001 HIS E 87 PHE 0.023 0.002 PHE E 198 TYR 0.020 0.003 TYR G 34 ARG 0.018 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.06219 ( 860) hydrogen bonds : angle 5.64093 ( 2403) covalent geometry : bond 0.00500 (15415) covalent geometry : angle 0.64484 (20966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28365.72 seconds wall clock time: 485 minutes 13.81 seconds (29113.81 seconds total)