Starting phenix.real_space_refine on Fri Jun 13 14:46:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_26921.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_26921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_26921.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_26921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzx_26921/06_2025/7uzx_26921.cif" } resolution = 3.49 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= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.10, per 1000 atoms: 0.68 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: 4.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.93 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: 4.43 Time building geometry restraints manager: 4.60 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: 8905 34.68 - 69.37: 211 69.37 - 104.05: 8 104.05 - 138.74: 2 138.74 - 173.42: 3 Dihedral angle restraints: 9129 sinusoidal: 4072 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 9126 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: 4.500 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.430 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 14.906 173.423 5876 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.12 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 (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: -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 TRP 0.009 0.001 TRP F 339 HIS 0.018 0.002 HIS D 62 PHE 0.025 0.002 PHE C 166 TYR 0.021 0.002 TYR C 206 ARG 0.021 0.001 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.13538 ( 628) hydrogen bonds : angle 6.08561 ( 1844) SS BOND : bond 0.00575 ( 1) SS BOND : angle 3.22869 ( 2) covalent geometry : bond 0.00667 (15188) covalent geometry : angle 0.90664 (20595) *********************** 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 : 1.915 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: 0.3311 time to fit residues: 131.1210 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 : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 129 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN F 60 HIS F 183 GLN F 295 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059230 restraints weight = 67156.660| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 5.96 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15189 Z= 0.150 Angle : 0.635 11.360 20597 Z= 0.336 Chirality : 0.044 0.203 2292 Planarity : 0.004 0.044 2536 Dihedral : 13.890 177.486 2413 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.87 % Allowed : 8.77 % Favored : 89.36 % 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: -0.25 (0.20), residues: 1718 helix: 1.12 (0.20), residues: 643 sheet: 0.53 (0.28), residues: 350 loop : -1.77 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 52 HIS 0.016 0.001 HIS A 72 PHE 0.019 0.001 PHE H 163 TYR 0.023 0.001 TYR H 255 ARG 0.007 0.001 ARG D 187 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 628) hydrogen bonds : angle 5.07484 ( 1844) SS BOND : bond 0.00109 ( 1) SS BOND : angle 2.00274 ( 2) covalent geometry : bond 0.00326 (15188) covalent geometry : angle 0.63461 (20595) *********************** 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 166 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.861 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 69 GLN cc_start: 0.7313 (mt0) cc_final: 0.6771 (mm110) REVERT: A 193 GLN cc_start: 0.8825 (mt0) cc_final: 0.8563 (mt0) REVERT: C 122 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8839 (ttmm) REVERT: C 193 GLN cc_start: 0.8441 (mt0) cc_final: 0.8148 (mm-40) REVERT: D 124 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7832 (tm-30) REVERT: D 200 GLU cc_start: 0.8554 (tt0) cc_final: 0.8080 (tm-30) REVERT: E 55 MET cc_start: 0.8585 (tpp) cc_final: 0.8362 (mmp) REVERT: E 82 LEU cc_start: 0.7203 (mm) cc_final: 0.6923 (tt) REVERT: H 129 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (mm-40) REVERT: H 214 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: H 258 MET cc_start: 0.6957 (tmm) cc_final: 0.6740 (tmm) REVERT: F 283 PHE cc_start: 0.8215 (t80) cc_final: 0.7969 (t80) REVERT: F 300 LEU cc_start: 0.9226 (mt) cc_final: 0.8654 (pp) outliers start: 29 outliers final: 10 residues processed: 159 average time/residue: 0.2928 time to fit residues: 68.0797 Evaluate side-chains 120 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 122 LYS 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 99 HIS Chi-restraints excluded: chain H residue 129 GLN Chi-restraints excluded: chain H residue 214 GLN 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 15 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN F 386 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.076846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053660 restraints weight = 70251.222| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 6.01 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 15189 Z= 0.406 Angle : 0.805 17.270 20597 Z= 0.426 Chirality : 0.049 0.467 2292 Planarity : 0.005 0.046 2536 Dihedral : 14.012 172.223 2413 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.13 % Allowed : 12.12 % Favored : 85.75 % 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: -0.65 (0.19), residues: 1718 helix: 0.83 (0.20), residues: 644 sheet: 0.26 (0.27), residues: 354 loop : -2.01 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 52 HIS 0.013 0.002 HIS A 72 PHE 0.017 0.002 PHE F 442 TYR 0.040 0.002 TYR F 21 ARG 0.009 0.001 ARG F 405 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 628) hydrogen bonds : angle 5.39618 ( 1844) SS BOND : bond 0.00335 ( 1) SS BOND : angle 3.62353 ( 2) covalent geometry : bond 0.00879 (15188) covalent geometry : angle 0.80412 (20595) *********************** 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 126 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8870 (mt0) cc_final: 0.8640 (mt0) REVERT: C 193 GLN cc_start: 0.8650 (mt0) cc_final: 0.8403 (mm-40) REVERT: D 40 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 124 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7877 (tm-30) REVERT: D 212 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8540 (tmtt) REVERT: F 163 MET cc_start: 0.8904 (mmm) cc_final: 0.8670 (mmt) REVERT: F 252 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8082 (p90) REVERT: F 283 PHE cc_start: 0.8602 (t80) cc_final: 0.8241 (t80) REVERT: F 300 LEU cc_start: 0.9299 (mt) cc_final: 0.8708 (pp) outliers start: 33 outliers final: 20 residues processed: 119 average time/residue: 0.2935 time to fit residues: 52.0078 Evaluate side-chains 100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 39 LEU 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 151 VAL Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 293 VAL 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 50 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 162 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.079001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056087 restraints weight = 66718.304| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 5.78 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15189 Z= 0.129 Angle : 0.570 12.723 20597 Z= 0.303 Chirality : 0.042 0.280 2292 Planarity : 0.003 0.044 2536 Dihedral : 13.672 178.166 2413 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.06 % Allowed : 13.22 % Favored : 84.72 % 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: -0.02 (0.20), residues: 1718 helix: 1.48 (0.20), residues: 644 sheet: 0.71 (0.28), residues: 335 loop : -1.81 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 PHE 0.015 0.001 PHE F 442 TYR 0.015 0.001 TYR F 21 ARG 0.006 0.000 ARG F 405 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 628) hydrogen bonds : angle 4.82758 ( 1844) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.70735 ( 2) covalent geometry : bond 0.00275 (15188) covalent geometry : angle 0.56995 (20595) *********************** 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 130 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASP cc_start: 0.8709 (t0) cc_final: 0.8429 (t0) REVERT: C 193 GLN cc_start: 0.8661 (mt0) cc_final: 0.8397 (mm-40) REVERT: D 124 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7895 (tm-30) REVERT: H 13 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8041 (pttm) REVERT: F 163 MET cc_start: 0.8891 (mmm) cc_final: 0.8524 (mmt) REVERT: F 252 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7897 (p90) REVERT: F 257 MET cc_start: 0.8622 (mpp) cc_final: 0.8415 (mpp) REVERT: F 283 PHE cc_start: 0.8304 (t80) cc_final: 0.7916 (t80) REVERT: F 300 LEU cc_start: 0.9250 (mt) cc_final: 0.8669 (pp) REVERT: F 352 MET cc_start: 0.7963 (ttp) cc_final: 0.7386 (ttp) outliers start: 32 outliers final: 19 residues processed: 121 average time/residue: 0.2834 time to fit residues: 51.7068 Evaluate side-chains 111 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 C residue 130 LEU 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 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 62 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 302 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 259 MET 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 156 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN H 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.079827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056735 restraints weight = 69262.314| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 6.37 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15189 Z= 0.112 Angle : 0.554 13.591 20597 Z= 0.292 Chirality : 0.042 0.396 2292 Planarity : 0.003 0.050 2536 Dihedral : 13.524 178.069 2413 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.13 % Allowed : 13.02 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.20), residues: 1718 helix: 1.70 (0.20), residues: 644 sheet: 0.91 (0.28), residues: 338 loop : -1.74 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 52 HIS 0.009 0.001 HIS A 72 PHE 0.012 0.001 PHE H 163 TYR 0.012 0.001 TYR F 21 ARG 0.006 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 628) hydrogen bonds : angle 4.64037 ( 1844) SS BOND : bond 0.00151 ( 1) SS BOND : angle 1.42025 ( 2) covalent geometry : bond 0.00239 (15188) covalent geometry : angle 0.55345 (20595) *********************** 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 134 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASP cc_start: 0.8604 (t0) cc_final: 0.8367 (t0) REVERT: A 193 GLN cc_start: 0.8869 (mt0) cc_final: 0.8231 (mm-40) REVERT: C 193 GLN cc_start: 0.8652 (mt0) cc_final: 0.8425 (mm-40) REVERT: D 124 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7898 (tm-30) REVERT: D 212 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (tmtt) REVERT: H 13 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7894 (pttm) REVERT: F 163 MET cc_start: 0.8850 (mmm) cc_final: 0.8600 (mmt) REVERT: F 283 PHE cc_start: 0.8214 (t80) cc_final: 0.7859 (t80) REVERT: F 300 LEU cc_start: 0.9229 (mt) cc_final: 0.8829 (tt) REVERT: F 352 MET cc_start: 0.7925 (ttp) cc_final: 0.7438 (ttp) outliers start: 33 outliers final: 13 residues processed: 130 average time/residue: 0.2593 time to fit residues: 51.7532 Evaluate side-chains 104 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 C residue 130 LEU Chi-restraints excluded: chain D residue 212 LYS 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 F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS 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 119 optimal weight: 0.0170 chunk 135 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.079243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056594 restraints weight = 68260.994| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.74 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15189 Z= 0.127 Angle : 0.540 13.562 20597 Z= 0.285 Chirality : 0.041 0.233 2292 Planarity : 0.003 0.053 2536 Dihedral : 13.439 177.297 2413 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 13.54 % Favored : 84.40 % 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: 0.31 (0.20), residues: 1718 helix: 1.79 (0.21), residues: 645 sheet: 0.98 (0.28), residues: 338 loop : -1.73 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 52 HIS 0.007 0.001 HIS H 287 PHE 0.011 0.001 PHE H 121 TYR 0.019 0.001 TYR H 255 ARG 0.004 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 628) hydrogen bonds : angle 4.53193 ( 1844) SS BOND : bond 0.00183 ( 1) SS BOND : angle 1.34859 ( 2) covalent geometry : bond 0.00276 (15188) covalent geometry : angle 0.53943 (20595) *********************** 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 125 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASP cc_start: 0.8653 (t0) cc_final: 0.8401 (t0) REVERT: A 193 GLN cc_start: 0.8887 (mt0) cc_final: 0.8357 (mm-40) REVERT: C 193 GLN cc_start: 0.8650 (mt0) cc_final: 0.8419 (mm-40) REVERT: D 212 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8571 (tmtt) REVERT: E 55 MET cc_start: 0.8281 (mmp) cc_final: 0.8061 (tpp) REVERT: H 13 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7863 (pttm) REVERT: F 163 MET cc_start: 0.8856 (mmm) cc_final: 0.8475 (mmt) REVERT: F 252 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7878 (p90) REVERT: F 283 PHE cc_start: 0.8212 (t80) cc_final: 0.7827 (t80) REVERT: F 300 LEU cc_start: 0.9238 (mt) cc_final: 0.8865 (tt) REVERT: F 452 MET cc_start: 0.7071 (tpt) cc_final: 0.6856 (tpt) outliers start: 32 outliers final: 22 residues processed: 118 average time/residue: 0.2770 time to fit residues: 50.0562 Evaluate side-chains 108 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 C residue 130 LEU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 66 LYS 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 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 262 ILE 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 24 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** 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 = 0.3673 r_free = 0.3673 target = 0.079097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056480 restraints weight = 68563.718| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.91 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15189 Z= 0.124 Angle : 0.532 15.460 20597 Z= 0.279 Chirality : 0.041 0.245 2292 Planarity : 0.003 0.053 2536 Dihedral : 13.332 177.576 2413 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.06 % Allowed : 13.93 % Favored : 84.01 % 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: 0.41 (0.20), residues: 1718 helix: 1.90 (0.21), residues: 645 sheet: 1.19 (0.28), residues: 308 loop : -1.66 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 PHE 0.011 0.001 PHE F 442 TYR 0.013 0.001 TYR F 21 ARG 0.005 0.000 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 628) hydrogen bonds : angle 4.45828 ( 1844) SS BOND : bond 0.00186 ( 1) SS BOND : angle 1.27605 ( 2) covalent geometry : bond 0.00267 (15188) covalent geometry : angle 0.53160 (20595) *********************** 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 118 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.9087 (p) REVERT: A 67 MET cc_start: 0.8335 (tmm) cc_final: 0.7884 (tmm) REVERT: A 179 ASP cc_start: 0.8752 (t0) cc_final: 0.8515 (t0) REVERT: A 193 GLN cc_start: 0.8910 (mt0) cc_final: 0.8345 (mm-40) REVERT: C 193 GLN cc_start: 0.8667 (mt0) cc_final: 0.8430 (mm-40) REVERT: D 40 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9086 (tm-30) REVERT: D 212 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8561 (tmtt) REVERT: E 55 MET cc_start: 0.8276 (mmp) cc_final: 0.8032 (tpp) REVERT: E 103 PHE cc_start: 0.6295 (m-80) cc_final: 0.5978 (m-80) REVERT: H 13 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: F 163 MET cc_start: 0.8801 (mmm) cc_final: 0.8407 (mmt) REVERT: F 252 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7896 (p90) REVERT: F 283 PHE cc_start: 0.8189 (t80) cc_final: 0.7841 (t80) REVERT: F 300 LEU cc_start: 0.9228 (mt) cc_final: 0.8871 (tt) REVERT: F 452 MET cc_start: 0.6895 (tpt) cc_final: 0.6642 (tpt) outliers start: 32 outliers final: 19 residues processed: 113 average time/residue: 0.3207 time to fit residues: 55.5701 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 : 1.547 ------------------------------------------------------------------------------- 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 C residue 130 LEU Chi-restraints excluded: chain D residue 17 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 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 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 151 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3660 r_free = 0.3660 target = 0.078633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056217 restraints weight = 69473.801| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 6.01 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5028 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= 0.146 Angle : 0.537 13.496 20597 Z= 0.283 Chirality : 0.041 0.213 2292 Planarity : 0.003 0.053 2536 Dihedral : 13.308 177.447 2413 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.81 % Allowed : 14.57 % Favored : 83.62 % 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: 0.41 (0.20), residues: 1718 helix: 1.93 (0.20), residues: 646 sheet: 1.05 (0.28), residues: 323 loop : -1.68 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 52 HIS 0.011 0.001 HIS E 174 PHE 0.010 0.001 PHE F 442 TYR 0.020 0.001 TYR D 206 ARG 0.005 0.000 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 628) hydrogen bonds : angle 4.47694 ( 1844) SS BOND : bond 0.00209 ( 1) SS BOND : angle 1.33924 ( 2) covalent geometry : bond 0.00318 (15188) covalent geometry : angle 0.53694 (20595) *********************** 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 107 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9145 (p) REVERT: A 67 MET cc_start: 0.8375 (tmm) cc_final: 0.7986 (tmm) REVERT: A 193 GLN cc_start: 0.8956 (mt0) cc_final: 0.8400 (mm-40) REVERT: C 193 GLN cc_start: 0.8679 (mt0) cc_final: 0.8429 (mm-40) REVERT: D 40 GLN cc_start: 0.9299 (tm-30) cc_final: 0.9072 (tm-30) REVERT: D 212 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8578 (tmtt) REVERT: E 55 MET cc_start: 0.8256 (mmp) cc_final: 0.7981 (tpp) REVERT: E 103 PHE cc_start: 0.6171 (m-80) cc_final: 0.5879 (m-80) REVERT: H 13 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7785 (pttm) REVERT: F 1 MET cc_start: 0.6309 (mmt) cc_final: 0.5982 (ttp) REVERT: F 163 MET cc_start: 0.8815 (mmm) cc_final: 0.8614 (mmt) REVERT: F 252 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7980 (p90) REVERT: F 257 MET cc_start: 0.8794 (mpp) cc_final: 0.8522 (mpp) REVERT: F 283 PHE cc_start: 0.8238 (t80) cc_final: 0.7874 (t80) REVERT: F 300 LEU cc_start: 0.9211 (mt) cc_final: 0.8901 (tt) REVERT: F 452 MET cc_start: 0.6795 (tpt) cc_final: 0.6049 (mmm) outliers start: 28 outliers final: 19 residues processed: 102 average time/residue: 0.2674 time to fit residues: 41.8405 Evaluate side-chains 99 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 17 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 99 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 65 optimal weight: 0.0470 chunk 7 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 159 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.079495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057193 restraints weight = 68298.540| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.72 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15189 Z= 0.098 Angle : 0.525 16.313 20597 Z= 0.275 Chirality : 0.041 0.244 2292 Planarity : 0.003 0.054 2536 Dihedral : 13.232 178.388 2413 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.48 % Allowed : 14.83 % Favored : 83.69 % 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: 0.49 (0.20), residues: 1718 helix: 1.94 (0.21), residues: 646 sheet: 1.26 (0.28), residues: 314 loop : -1.63 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 52 HIS 0.007 0.001 HIS A 72 PHE 0.011 0.001 PHE F 283 TYR 0.012 0.001 TYR F 463 ARG 0.005 0.000 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 628) hydrogen bonds : angle 4.41268 ( 1844) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.15909 ( 2) covalent geometry : bond 0.00209 (15188) covalent geometry : angle 0.52472 (20595) *********************** 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 115 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9047 (p) REVERT: A 67 MET cc_start: 0.8420 (tmm) cc_final: 0.8005 (tmm) REVERT: A 193 GLN cc_start: 0.8948 (mt0) cc_final: 0.8412 (mm-40) REVERT: C 193 GLN cc_start: 0.8657 (mt0) cc_final: 0.8414 (mm-40) REVERT: D 40 GLN cc_start: 0.9288 (tm-30) cc_final: 0.9048 (tm-30) REVERT: E 55 MET cc_start: 0.8269 (mmp) cc_final: 0.8007 (tpp) REVERT: E 103 PHE cc_start: 0.6444 (m-80) cc_final: 0.6150 (m-80) REVERT: H 13 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7774 (pttm) REVERT: F 1 MET cc_start: 0.6314 (mmt) cc_final: 0.5979 (ttp) REVERT: F 252 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7924 (p90) REVERT: F 283 PHE cc_start: 0.8113 (t80) cc_final: 0.7810 (t80) REVERT: F 300 LEU cc_start: 0.9173 (mt) cc_final: 0.8909 (tt) REVERT: F 452 MET cc_start: 0.6483 (tpt) cc_final: 0.6195 (tpt) outliers start: 23 outliers final: 19 residues processed: 111 average time/residue: 0.2648 time to fit residues: 46.9561 Evaluate side-chains 102 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 C residue 130 LEU 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 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 201 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** 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 = 0.3641 r_free = 0.3641 target = 0.077754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.055583 restraints weight = 69786.347| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.61 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15189 Z= 0.195 Angle : 0.593 14.642 20597 Z= 0.311 Chirality : 0.042 0.165 2292 Planarity : 0.003 0.068 2536 Dihedral : 13.341 175.852 2413 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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 (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: 0.38 (0.20), residues: 1718 helix: 1.88 (0.21), residues: 646 sheet: 1.10 (0.28), residues: 323 loop : -1.69 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 52 HIS 0.012 0.001 HIS E 174 PHE 0.012 0.001 PHE A 166 TYR 0.023 0.001 TYR D 206 ARG 0.009 0.000 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 628) hydrogen bonds : angle 4.59373 ( 1844) SS BOND : bond 0.00270 ( 1) SS BOND : angle 1.47157 ( 2) covalent geometry : bond 0.00427 (15188) covalent geometry : angle 0.59293 (20595) ********************** 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: 24 poor density : 81 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8443 (tmm) cc_final: 0.8055 (tmm) REVERT: A 193 GLN cc_start: 0.8968 (mt0) cc_final: 0.8442 (mm-40) REVERT: C 193 GLN cc_start: 0.8731 (mt0) cc_final: 0.8479 (mm-40) REVERT: E 55 MET cc_start: 0.8264 (mmp) cc_final: 0.7983 (tpp) REVERT: E 103 PHE cc_start: 0.6370 (m-80) cc_final: 0.6110 (m-80) REVERT: H 13 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7768 (pttm) REVERT: F 1 MET cc_start: 0.6526 (mmt) cc_final: 0.6164 (ttp) REVERT: F 252 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7999 (p90) REVERT: F 283 PHE cc_start: 0.8279 (t80) cc_final: 0.7961 (t80) REVERT: F 300 LEU cc_start: 0.9211 (mt) cc_final: 0.8843 (tt) REVERT: F 452 MET cc_start: 0.6579 (tpt) cc_final: 0.6213 (tpt) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.2692 time to fit residues: 41.7723 Evaluate side-chains 100 residues out of total 1551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 C residue 130 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE 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 E residue 201 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 51 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.078416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056126 restraints weight = 70048.517| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.91 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15189 Z= 0.142 Angle : 0.576 16.416 20597 Z= 0.303 Chirality : 0.041 0.158 2292 Planarity : 0.004 0.104 2536 Dihedral : 13.346 177.083 2413 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.29 % Allowed : 15.86 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.20), residues: 1718 helix: 1.87 (0.21), residues: 645 sheet: 1.15 (0.28), residues: 315 loop : -1.66 (0.19), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 189 HIS 0.029 0.001 HIS C 72 PHE 0.011 0.001 PHE F 442 TYR 0.015 0.001 TYR F 21 ARG 0.014 0.000 ARG E 81 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 628) hydrogen bonds : angle 4.55430 ( 1844) SS BOND : bond 0.00217 ( 1) SS BOND : angle 1.39200 ( 2) covalent geometry : bond 0.00308 (15188) covalent geometry : angle 0.57554 (20595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6283.00 seconds wall clock time: 109 minutes 30.57 seconds (6570.57 seconds total)