Starting phenix.real_space_refine on Fri Jul 3 16:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzx_26921/07_2026/7uzx_26921.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 P 36 5.49 5 S 32 5.16 5 C 9246 2.51 5 N 2552 2.21 5 O 2992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14858 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1458 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain breaks: 2 Chain: "H" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2355 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3886 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 5, 'TRANS': 472} Chain breaks: 6 Chain: "G" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 11, 'rna3p': 19} Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Time building chain proxies: 3.70, per 1000 atoms: 0.25 Number of scatterers: 14858 At special positions: 0 Unit cell: (92.4, 116.6, 204.6, 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 32 16.00 P 36 15.00 O 2992 8.00 N 2552 7.00 C 9246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 775.7 milliseconds 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 21 sheets defined 39.8% alpha, 21.1% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.844A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.630A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.899A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.996A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.631A pdb=" N ARG C 187 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.689A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'E' and resid 47 through 63 removed outlier: 3.754A pdb=" N ILE E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 76 through 83 Processing helix chain 'E' and resid 104 through 115 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 50 through 55 removed outlier: 3.961A pdb=" N ASN H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.503A pdb=" N LEU H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 228 through 236 removed outlier: 4.446A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.872A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.176A pdb=" N SER F 29 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.934A pdb=" N TYR F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.857A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 154 through 170 Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 205 through 227 removed outlier: 3.613A pdb=" N HIS F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.524A pdb=" N GLN F 248 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 279 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.784A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 386 removed outlier: 4.263A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 423 through 437 Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.680A pdb=" N THR F 539 " --> pdb=" O ASN F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 567 removed outlier: 3.633A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 574 Processing helix chain 'F' and resid 595 through 612 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.148A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A 3 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS A 4 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR A 10 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP A 196 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 14 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE A 192 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 127 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.539A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.453A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.751A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.751A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.190A pdb=" N VAL D 151 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA D 101 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP D 149 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 103 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLU D 147 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.202A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER E 8 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR E 197 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.990A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS E 6 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR E 201 " --> pdb=" O LYS E 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 71 " --> pdb=" O PRO H 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AB7, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'H' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.591A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'F' and resid 307 through 311 removed outlier: 5.900A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.958A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4777 1.34 - 1.47: 3798 1.47 - 1.60: 6519 1.60 - 1.72: 36 1.72 - 1.85: 58 Bond restraints: 15188 Sorted by residual: bond pdb=" O3' G G 20 " pdb=" P U G 21 " ideal model delta sigma weight residual 1.607 1.737 -0.130 1.50e-02 4.44e+03 7.52e+01 bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.70e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.555 -0.085 1.50e-02 4.44e+03 3.20e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.470 1.549 -0.079 1.50e-02 4.44e+03 2.78e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.401 0.074 1.50e-02 4.44e+03 2.42e+01 ... (remaining 15183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.24: 20591 11.24 - 22.49: 3 22.49 - 33.73: 0 33.73 - 44.98: 0 44.98 - 56.22: 1 Bond angle restraints: 20595 Sorted by residual: angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" OP2 U G 21 " ideal model delta sigma weight residual 108.00 51.78 56.22 3.00e+00 1.11e-01 3.51e+02 angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" O5' U G 21 " ideal model delta sigma weight residual 104.00 123.70 -19.70 1.50e+00 4.44e-01 1.72e+02 angle pdb=" O3' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " ideal model delta sigma weight residual 109.50 121.01 -11.51 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" OP1 U G 21 " ideal model delta sigma weight residual 108.00 128.78 -20.78 3.00e+00 1.11e-01 4.80e+01 angle pdb=" C3' G G 20 " pdb=" O3' G G 20 " pdb=" P U G 21 " ideal model delta sigma weight residual 120.20 129.98 -9.78 1.50e+00 4.44e-01 4.25e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 8861 34.68 - 69.37: 163 69.37 - 104.05: 4 104.05 - 138.74: 2 138.74 - 173.42: 3 Dihedral angle restraints: 9033 sinusoidal: 3976 harmonic: 5057 Sorted by residual: dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 43.39 -171.39 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -41.41 -118.59 1 1.50e+01 4.44e-03 6.31e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -147.96 61.96 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2066 0.086 - 0.171: 212 0.171 - 0.257: 13 0.257 - 0.342: 0 0.342 - 0.427: 1 Chirality restraints: 2292 Sorted by residual: chirality pdb=" C3' U G 15 " pdb=" C4' U G 15 " pdb=" O3' U G 15 " pdb=" C2' U G 15 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA SER B 33 " pdb=" N SER B 33 " pdb=" C SER B 33 " pdb=" CB SER B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P A G 14 " pdb=" OP1 A G 14 " pdb=" OP2 A G 14 " pdb=" O5' A G 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.17 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2289 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 252 " 0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C PHE F 252 " -0.094 2.00e-02 2.50e+03 pdb=" O PHE F 252 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU F 253 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 15 " -0.028 2.00e-02 2.50e+03 2.52e-02 1.43e+01 pdb=" N1 U G 15 " 0.066 2.00e-02 2.50e+03 pdb=" C2 U G 15 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U G 15 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U G 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U G 15 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U G 15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U G 15 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 134 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA A 134 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA A 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 135 " 0.021 2.00e-02 2.50e+03 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 69 2.47 - 3.08: 10025 3.08 - 3.69: 20694 3.69 - 4.29: 30370 4.29 - 4.90: 51197 Nonbonded interactions: 112355 Sorted by model distance: nonbonded pdb=" C3' G G 20 " pdb=" OP2 U G 21 " model vdw 1.865 2.776 nonbonded pdb=" ND2 ASN D 57 " pdb=" C5 U G 26 " model vdw 1.943 3.420 nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.967 3.120 nonbonded pdb=" OG1 THR B 126 " pdb=" OD1 ASN B 135 " model vdw 2.060 3.040 nonbonded pdb=" OG1 THR D 186 " pdb=" OP1 U G 30 " model vdw 2.160 3.040 ... (remaining 112350 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 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'B' and (resid 2 through 23 or resid 33 through 120 or resid 141 through \ 214)) selection = (chain 'C' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'D' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'E' and (resid 2 through 63 or resid 76 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.960 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.007 0.130 15189 Z= 0.326 Angle : 0.907 56.223 20597 Z= 0.485 Chirality : 0.052 0.427 2292 Planarity : 0.004 0.054 2536 Dihedral : 13.978 173.423 5780 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 1718 helix: 0.56 (0.21), residues: 632 sheet: 0.14 (0.28), residues: 343 loop : -1.99 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 187 TYR 0.021 0.002 TYR C 206 PHE 0.025 0.002 PHE C 166 TRP 0.009 0.001 TRP F 339 HIS 0.018 0.002 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.33 (15188) covalent geometry : angle 0.90664 / 0.48 (20595) SS BOND : bond 0.00575 / 0.30 ( 1) SS BOND : angle 3.22869 / 1.76 ( 2) hydrogen bonds : bond 0.13538 / 8.96 ( 628) hydrogen bonds : angle 6.08561 / 4.22 ( 1844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.1535 time to fit residues: 61.6228 Evaluate side-chains 118 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 138 GLN B 193 GLN C 69 GLN C 174 HIS ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 87 HIS H 129 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 295 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.080874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058128 restraints weight = 67381.631| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 6.01 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15189 Z= 0.195 Angle : 0.654 12.193 20597 Z= 0.348 Chirality : 0.044 0.237 2292 Planarity : 0.004 0.047 2536 Dihedral : 11.576 176.105 2317 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.93 % Allowed : 9.16 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.20), residues: 1718 helix: 1.07 (0.20), residues: 644 sheet: 0.46 (0.28), residues: 351 loop : -1.84 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 137 TYR 0.021 0.001 TYR H 255 PHE 0.024 0.002 PHE H 163 TRP 0.023 0.002 TRP F 184 HIS 0.017 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (15188) covalent geometry : angle 0.65325 / 0.35 (20595) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 2.11630 / 1.16 ( 2) hydrogen bonds : bond 0.04575 / 3.10 ( 628) hydrogen bonds : angle 5.12931 / 3.54 ( 1844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8834 (mt0) cc_final: 0.8567 (mt0) REVERT: C 193 GLN cc_start: 0.8497 (mt0) cc_final: 0.8210 (mm-40) REVERT: D 124 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7872 (tm-30) REVERT: E 55 MET cc_start: 0.8580 (tpp) cc_final: 0.8356 (mmp) REVERT: E 82 LEU cc_start: 0.7178 (mm) cc_final: 0.6930 (tt) REVERT: H 13 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7740 (pttp) REVERT: H 129 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8627 (mm-40) REVERT: H 214 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: F 283 PHE cc_start: 0.8284 (t80) cc_final: 0.8025 (t80) REVERT: F 300 LEU cc_start: 0.9246 (mt) cc_final: 0.8651 (pp) outliers start: 30 outliers final: 11 residues processed: 148 average time/residue: 0.1337 time to fit residues: 29.3497 Evaluate side-chains 111 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 214 GLN Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 chunk 147 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN D 97 GLN H 17 HIS H 129 GLN H 214 GLN F 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.081771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058596 restraints weight = 66839.553| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 6.04 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15189 Z= 0.114 Angle : 0.562 12.490 20597 Z= 0.298 Chirality : 0.042 0.197 2292 Planarity : 0.003 0.041 2536 Dihedral : 11.283 177.745 2317 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.48 % Allowed : 10.64 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1718 helix: 1.40 (0.21), residues: 644 sheet: 0.70 (0.29), residues: 334 loop : -1.71 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.012 0.001 TYR D 154 PHE 0.016 0.001 PHE F 442 TRP 0.018 0.001 TRP H 52 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15188) covalent geometry : angle 0.56145 / 0.30 (20595) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 1.71952 / 0.94 ( 2) hydrogen bonds : bond 0.03815 / 2.57 ( 628) hydrogen bonds : angle 4.80607 / 3.31 ( 1844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8881 (mt0) cc_final: 0.8627 (mt0) REVERT: C 193 GLN cc_start: 0.8533 (mt0) cc_final: 0.8245 (mm-40) REVERT: D 40 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8902 (tm-30) REVERT: D 124 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7912 (tm-30) REVERT: E 82 LEU cc_start: 0.6929 (mm) cc_final: 0.6659 (tt) REVERT: H 13 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7233 (ptpp) REVERT: F 78 THR cc_start: 0.8262 (m) cc_final: 0.7990 (p) REVERT: F 257 MET cc_start: 0.8709 (mpp) cc_final: 0.8499 (mpp) REVERT: F 283 PHE cc_start: 0.8236 (t80) cc_final: 0.7912 (t80) REVERT: F 300 LEU cc_start: 0.9250 (mt) cc_final: 0.8693 (pp) outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 0.1335 time to fit residues: 26.0124 Evaluate side-chains 106 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 151 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.079127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056141 restraints weight = 67557.328| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.84 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15189 Z= 0.200 Angle : 0.593 13.334 20597 Z= 0.314 Chirality : 0.043 0.314 2292 Planarity : 0.003 0.041 2536 Dihedral : 11.279 175.521 2317 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.61 % Allowed : 12.19 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1718 helix: 1.53 (0.21), residues: 646 sheet: 0.81 (0.28), residues: 337 loop : -1.80 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 405 TYR 0.020 0.001 TYR F 21 PHE 0.017 0.001 PHE H 163 TRP 0.014 0.001 TRP H 52 HIS 0.012 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (15188) covalent geometry : angle 0.59309 / 0.31 (20595) SS BOND : bond 0.00302 / 0.16 ( 1) SS BOND : angle 1.86569 / 1.04 ( 2) hydrogen bonds : bond 0.04076 / 2.81 ( 628) hydrogen bonds : angle 4.74534 / 3.27 ( 1844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 193 GLN cc_start: 0.8596 (mt0) cc_final: 0.8323 (mm-40) REVERT: D 124 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7879 (tm-30) REVERT: F 252 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7707 (p90) REVERT: F 257 MET cc_start: 0.8758 (mpp) cc_final: 0.8556 (mpp) REVERT: F 283 PHE cc_start: 0.8283 (t80) cc_final: 0.7908 (t80) REVERT: F 300 LEU cc_start: 0.9237 (mt) cc_final: 0.8811 (tt) outliers start: 25 outliers final: 15 residues processed: 114 average time/residue: 0.1275 time to fit residues: 22.0061 Evaluate side-chains 99 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.079341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056349 restraints weight = 68507.338| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.94 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15189 Z= 0.174 Angle : 0.570 13.536 20597 Z= 0.300 Chirality : 0.042 0.246 2292 Planarity : 0.003 0.042 2536 Dihedral : 11.193 177.090 2317 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.19 % Allowed : 12.70 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1718 helix: 1.65 (0.20), residues: 645 sheet: 0.78 (0.28), residues: 339 loop : -1.80 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 405 TYR 0.018 0.001 TYR F 21 PHE 0.026 0.001 PHE H 163 TRP 0.014 0.001 TRP H 52 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (15188) covalent geometry : angle 0.56934 / 0.30 (20595) SS BOND : bond 0.00297 / 0.16 ( 1) SS BOND : angle 1.59729 / 0.88 ( 2) hydrogen bonds : bond 0.03775 / 2.58 ( 628) hydrogen bonds : angle 4.64247 / 3.20 ( 1844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.9104 (p) REVERT: A 67 MET cc_start: 0.8416 (tmm) cc_final: 0.7915 (tmm) REVERT: A 193 GLN cc_start: 0.8756 (mt0) cc_final: 0.8324 (mm-40) REVERT: C 193 GLN cc_start: 0.8678 (mt0) cc_final: 0.8428 (mm-40) REVERT: D 124 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7862 (tm-30) REVERT: D 212 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8505 (tmtt) REVERT: E 55 MET cc_start: 0.8349 (mmp) cc_final: 0.8133 (tpp) REVERT: F 252 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7785 (p90) REVERT: F 257 MET cc_start: 0.8824 (mpp) cc_final: 0.8552 (mpp) REVERT: F 283 PHE cc_start: 0.8228 (t80) cc_final: 0.7897 (t80) REVERT: F 300 LEU cc_start: 0.9236 (mt) cc_final: 0.8822 (tt) outliers start: 34 outliers final: 16 residues processed: 115 average time/residue: 0.1222 time to fit residues: 21.7503 Evaluate side-chains 102 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 87 HIS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.078907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055726 restraints weight = 68864.540| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 6.07 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15189 Z= 0.165 Angle : 0.561 13.721 20597 Z= 0.295 Chirality : 0.042 0.256 2292 Planarity : 0.003 0.050 2536 Dihedral : 11.137 176.836 2317 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.00 % Allowed : 13.54 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1718 helix: 1.71 (0.20), residues: 652 sheet: 1.11 (0.29), residues: 308 loop : -1.78 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 405 TYR 0.020 0.001 TYR D 206 PHE 0.020 0.001 PHE H 163 TRP 0.015 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (15188) covalent geometry : angle 0.56108 / 0.29 (20595) SS BOND : bond 0.00293 / 0.15 ( 1) SS BOND : angle 1.52406 / 0.84 ( 2) hydrogen bonds : bond 0.03744 / 2.56 ( 628) hydrogen bonds : angle 4.55767 / 3.14 ( 1844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8561 (tmm) cc_final: 0.8192 (tmm) REVERT: A 193 GLN cc_start: 0.8841 (mt0) cc_final: 0.8356 (mm-40) REVERT: C 193 GLN cc_start: 0.8702 (mt0) cc_final: 0.8470 (mm-40) REVERT: D 212 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (tmtt) REVERT: E 55 MET cc_start: 0.8282 (mmp) cc_final: 0.8006 (tpp) REVERT: F 252 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7751 (p90) REVERT: F 257 MET cc_start: 0.8781 (mpp) cc_final: 0.8511 (mpp) REVERT: F 283 PHE cc_start: 0.8262 (t80) cc_final: 0.7897 (t80) REVERT: F 300 LEU cc_start: 0.9237 (mt) cc_final: 0.8864 (tt) outliers start: 31 outliers final: 21 residues processed: 113 average time/residue: 0.1208 time to fit residues: 21.0054 Evaluate side-chains 104 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.078579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055715 restraints weight = 68342.039| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 5.85 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15189 Z= 0.164 Angle : 0.562 15.279 20597 Z= 0.296 Chirality : 0.041 0.203 2292 Planarity : 0.003 0.057 2536 Dihedral : 11.098 176.925 2317 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.00 % Allowed : 13.93 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1718 helix: 1.85 (0.21), residues: 643 sheet: 0.99 (0.28), residues: 317 loop : -1.76 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 405 TYR 0.017 0.001 TYR F 21 PHE 0.016 0.001 PHE H 163 TRP 0.013 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (15188) covalent geometry : angle 0.56230 / 0.30 (20595) SS BOND : bond 0.00294 / 0.15 ( 1) SS BOND : angle 1.45739 / 0.80 ( 2) hydrogen bonds : bond 0.03704 / 2.53 ( 628) hydrogen bonds : angle 4.54788 / 3.13 ( 1844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9340 (OUTLIER) cc_final: 0.9136 (p) REVERT: A 67 MET cc_start: 0.8587 (tmm) cc_final: 0.8273 (tmm) REVERT: A 193 GLN cc_start: 0.8911 (mt0) cc_final: 0.8432 (mm-40) REVERT: C 193 GLN cc_start: 0.8709 (mt0) cc_final: 0.8471 (mm-40) REVERT: D 212 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (tmtt) REVERT: F 252 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7849 (p90) REVERT: F 257 MET cc_start: 0.8760 (mpp) cc_final: 0.8491 (mpp) REVERT: F 283 PHE cc_start: 0.8199 (t80) cc_final: 0.7881 (t80) REVERT: F 300 LEU cc_start: 0.9252 (mt) cc_final: 0.8875 (tt) REVERT: F 452 MET cc_start: 0.6784 (tpt) cc_final: 0.6562 (mmm) REVERT: F 468 MET cc_start: 0.9223 (mmt) cc_final: 0.9019 (ptt) outliers start: 31 outliers final: 22 residues processed: 110 average time/residue: 0.1160 time to fit residues: 19.9800 Evaluate side-chains 100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 253 THR Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 106 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.078081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055371 restraints weight = 69125.932| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 5.73 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15189 Z= 0.177 Angle : 0.579 13.659 20597 Z= 0.303 Chirality : 0.042 0.209 2292 Planarity : 0.003 0.056 2536 Dihedral : 11.105 176.649 2317 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.87 % Allowed : 14.25 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1718 helix: 1.79 (0.21), residues: 644 sheet: 0.99 (0.28), residues: 317 loop : -1.78 (0.19), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 405 TYR 0.022 0.001 TYR D 206 PHE 0.011 0.001 PHE H 121 TRP 0.017 0.002 TRP H 52 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (15188) covalent geometry : angle 0.57842 / 0.30 (20595) SS BOND : bond 0.00322 / 0.17 ( 1) SS BOND : angle 1.44367 / 0.79 ( 2) hydrogen bonds : bond 0.03798 / 2.60 ( 628) hydrogen bonds : angle 4.59901 / 3.17 ( 1844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8564 (tmm) cc_final: 0.8259 (tmm) REVERT: A 193 GLN cc_start: 0.8940 (mt0) cc_final: 0.8469 (mm-40) REVERT: C 193 GLN cc_start: 0.8729 (mt0) cc_final: 0.8488 (mm-40) REVERT: D 212 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (tmtt) REVERT: E 55 MET cc_start: 0.8283 (mmp) cc_final: 0.8055 (tpp) REVERT: E 103 PHE cc_start: 0.6302 (m-80) cc_final: 0.6060 (m-80) REVERT: F 1 MET cc_start: 0.6316 (mmt) cc_final: 0.5990 (ttp) REVERT: F 252 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7882 (p90) REVERT: F 257 MET cc_start: 0.8759 (mpp) cc_final: 0.8471 (mpp) REVERT: F 283 PHE cc_start: 0.8324 (t80) cc_final: 0.7946 (t80) REVERT: F 300 LEU cc_start: 0.9239 (mt) cc_final: 0.8880 (tt) REVERT: F 452 MET cc_start: 0.6825 (tpt) cc_final: 0.6452 (tpt) outliers start: 29 outliers final: 22 residues processed: 99 average time/residue: 0.1223 time to fit residues: 18.8086 Evaluate side-chains 98 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 82 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.078621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056190 restraints weight = 69462.424| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 5.94 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15189 Z= 0.124 Angle : 0.553 15.990 20597 Z= 0.288 Chirality : 0.041 0.192 2292 Planarity : 0.003 0.057 2536 Dihedral : 11.056 177.570 2317 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 14.57 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1718 helix: 1.88 (0.21), residues: 643 sheet: 1.24 (0.29), residues: 300 loop : -1.71 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 405 TYR 0.018 0.001 TYR H 125 PHE 0.011 0.001 PHE F 442 TRP 0.015 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15188) covalent geometry : angle 0.55237 / 0.29 (20595) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 1.35023 / 0.74 ( 2) hydrogen bonds : bond 0.03428 / 2.34 ( 628) hydrogen bonds : angle 4.49200 / 3.09 ( 1844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8571 (tmm) cc_final: 0.8268 (tmm) REVERT: A 193 GLN cc_start: 0.8939 (mt0) cc_final: 0.8533 (mm-40) REVERT: C 193 GLN cc_start: 0.8700 (mt0) cc_final: 0.8458 (mm-40) REVERT: E 55 MET cc_start: 0.8247 (mmp) cc_final: 0.7996 (tpp) REVERT: E 103 PHE cc_start: 0.6491 (m-80) cc_final: 0.6235 (m-80) REVERT: F 1 MET cc_start: 0.6394 (mmt) cc_final: 0.6076 (ttp) REVERT: F 252 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7806 (p90) REVERT: F 257 MET cc_start: 0.8723 (mpp) cc_final: 0.8448 (mpp) REVERT: F 283 PHE cc_start: 0.8156 (t80) cc_final: 0.7816 (t80) REVERT: F 300 LEU cc_start: 0.9217 (mt) cc_final: 0.8870 (tt) REVERT: F 452 MET cc_start: 0.6414 (tpt) cc_final: 0.6006 (tpt) outliers start: 24 outliers final: 19 residues processed: 103 average time/residue: 0.1080 time to fit residues: 17.6830 Evaluate side-chains 94 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 128 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 53 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.078682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056235 restraints weight = 68999.750| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 6.11 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15189 Z= 0.120 Angle : 0.553 14.738 20597 Z= 0.287 Chirality : 0.041 0.198 2292 Planarity : 0.003 0.057 2536 Dihedral : 11.050 177.489 2317 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.61 % Allowed : 14.96 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1718 helix: 1.88 (0.21), residues: 646 sheet: 1.10 (0.29), residues: 310 loop : -1.61 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 405 TYR 0.022 0.001 TYR D 206 PHE 0.011 0.001 PHE F 442 TRP 0.021 0.002 TRP H 52 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15188) covalent geometry : angle 0.55266 / 0.29 (20595) SS BOND : bond 0.00198 / 0.10 ( 1) SS BOND : angle 1.23259 / 0.68 ( 2) hydrogen bonds : bond 0.03371 / 2.29 ( 628) hydrogen bonds : angle 4.44584 / 3.05 ( 1844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8486 (tmm) cc_final: 0.8179 (tmm) REVERT: A 193 GLN cc_start: 0.8932 (mt0) cc_final: 0.8548 (mm-40) REVERT: C 193 GLN cc_start: 0.8708 (mt0) cc_final: 0.8476 (mm-40) REVERT: E 55 MET cc_start: 0.8271 (mmp) cc_final: 0.8030 (tpp) REVERT: E 103 PHE cc_start: 0.6369 (m-80) cc_final: 0.6140 (m-80) REVERT: H 28 MET cc_start: 0.8468 (ttm) cc_final: 0.7969 (tpp) REVERT: F 1 MET cc_start: 0.6481 (mmt) cc_final: 0.6207 (ttp) REVERT: F 252 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7825 (p90) REVERT: F 257 MET cc_start: 0.8714 (mpp) cc_final: 0.8459 (mpp) REVERT: F 283 PHE cc_start: 0.8157 (t80) cc_final: 0.7821 (t80) REVERT: F 300 LEU cc_start: 0.9208 (mt) cc_final: 0.8869 (tt) REVERT: F 452 MET cc_start: 0.6490 (tpt) cc_final: 0.6117 (tpt) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.1113 time to fit residues: 17.7421 Evaluate side-chains 97 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 0.0060 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.078745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055979 restraints weight = 69631.004| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 6.11 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15189 Z= 0.134 Angle : 0.563 16.304 20597 Z= 0.293 Chirality : 0.041 0.233 2292 Planarity : 0.003 0.057 2536 Dihedral : 11.058 177.239 2317 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 15.34 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1718 helix: 1.88 (0.21), residues: 646 sheet: 1.06 (0.28), residues: 320 loop : -1.64 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 405 TYR 0.015 0.001 TYR F 463 PHE 0.016 0.001 PHE H 163 TRP 0.020 0.002 TRP H 52 HIS 0.012 0.001 HIS E 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (15188) covalent geometry : angle 0.56333 / 0.29 (20595) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.23549 / 0.68 ( 2) hydrogen bonds : bond 0.03429 / 2.34 ( 628) hydrogen bonds : angle 4.43259 / 3.04 ( 1844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.12 seconds wall clock time: 51 minutes 56.19 seconds (3116.19 seconds total)