Starting phenix.real_space_refine on Fri Aug 7 04:01:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nlx_49525/08_2026/9nlx_49525.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 423 5.49 5 S 21 5.16 5 C 11079 2.51 5 N 3438 2.21 5 O 4809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19770 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3589 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 463} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 18, 'GLN:plan1': 4, 'ARG:plan': 9, 'ASP:plan': 14, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 211 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 3001 Classifications: {'RNA': 141} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 18, 'rna3p_pur': 59, 'rna3p_pyr': 52} Link IDs: {'rna2p': 30, 'rna3p': 110} Restraints were copied for chains: B, C, H, I Time building chain proxies: 5.66, per 1000 atoms: 0.29 Number of scatterers: 19770 At special positions: 0 Unit cell: (192.093, 179.408, 86.0795, 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 21 16.00 P 423 15.00 O 4809 8.00 N 3438 7.00 C 11079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 600.7 milliseconds 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 61.7% alpha, 6.7% beta 48 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 2 through 40 removed outlier: 3.666A pdb=" N ARG A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS A 30 " --> pdb=" O HIS A 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 removed outlier: 3.860A pdb=" N ALA A 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.766A pdb=" N SER A 56 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 110 through 128 Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.993A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.516A pdb=" N PHE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.263A pdb=" N PHE A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 316 through 336 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.979A pdb=" N LYS A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 removed outlier: 3.964A pdb=" N LEU A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 404 through 433 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.734A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 484 removed outlier: 4.003A pdb=" N ILE A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 2 through 40 removed outlier: 3.666A pdb=" N ARG B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 14 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS B 30 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 removed outlier: 3.861A pdb=" N ALA B 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.766A pdb=" N SER B 56 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 110 through 128 Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.993A pdb=" N ALA B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.516A pdb=" N PHE B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 216 through 226 removed outlier: 4.263A pdb=" N PHE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.978A pdb=" N LYS B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 removed outlier: 3.964A pdb=" N LEU B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 404 through 433 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.734A pdb=" N LYS B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 484 removed outlier: 4.002A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 2 through 40 removed outlier: 3.666A pdb=" N ARG C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS C 30 " --> pdb=" O HIS C 26 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 removed outlier: 3.861A pdb=" N ALA C 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.766A pdb=" N SER C 56 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 71 through 84 Processing helix chain 'C' and resid 110 through 128 Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.993A pdb=" N ALA C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.516A pdb=" N PHE C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 216 through 226 removed outlier: 4.262A pdb=" N PHE C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 253 through 272 Processing helix chain 'C' and resid 316 through 336 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.978A pdb=" N LYS C 341 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 370 removed outlier: 3.964A pdb=" N LEU C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 393 through 398 Processing helix chain 'C' and resid 404 through 433 Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.734A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.003A pdb=" N ILE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 243 removed outlier: 3.667A pdb=" N LYS A 239 " --> pdb=" O TRP A 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 167 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A 282 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LYS A 298 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 285 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243 removed outlier: 3.667A pdb=" N LYS B 239 " --> pdb=" O TRP B 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 167 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 282 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS B 298 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 285 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AA8, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.667A pdb=" N LYS C 239 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 167 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY C 282 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LYS C 298 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 285 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 303 630 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 108 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 4.17 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3580 1.33 - 1.45: 7148 1.45 - 1.57: 9477 1.57 - 1.69: 843 1.69 - 1.81: 27 Bond restraints: 21075 Sorted by residual: bond pdb=" C ARG A 75 " pdb=" N SER A 76 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.31e-02 5.83e+03 3.09e+01 bond pdb=" C ARG B 75 " pdb=" N SER B 76 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.31e-02 5.83e+03 3.09e+01 bond pdb=" C ARG C 75 " pdb=" N SER C 76 " ideal model delta sigma weight residual 1.335 1.262 0.073 1.31e-02 5.83e+03 3.09e+01 bond pdb=" C ALA B 74 " pdb=" N ARG B 75 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.27e-02 6.20e+03 2.68e+01 bond pdb=" C ALA A 74 " pdb=" N ARG A 75 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.27e-02 6.20e+03 2.67e+01 ... (remaining 21070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 28128 1.40 - 2.79: 2154 2.79 - 4.19: 282 4.19 - 5.58: 51 5.58 - 6.98: 12 Bond angle restraints: 30627 Sorted by residual: angle pdb=" C3' A I 46 " pdb=" O3' A I 46 " pdb=" P A I 47 " ideal model delta sigma weight residual 119.70 126.35 -6.65 1.20e+00 6.94e-01 3.07e+01 angle pdb=" C3' A H 46 " pdb=" O3' A H 46 " pdb=" P A H 47 " ideal model delta sigma weight residual 119.70 126.33 -6.63 1.20e+00 6.94e-01 3.05e+01 angle pdb=" C3' A G 46 " pdb=" O3' A G 46 " pdb=" P A G 47 " ideal model delta sigma weight residual 119.70 126.33 -6.63 1.20e+00 6.94e-01 3.05e+01 angle pdb=" O5' C G 53 " pdb=" C5' C G 53 " pdb=" C4' C G 53 " ideal model delta sigma weight residual 109.40 113.63 -4.23 8.00e-01 1.56e+00 2.79e+01 angle pdb=" O5' C I 53 " pdb=" C5' C I 53 " pdb=" C4' C I 53 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.79e+01 ... (remaining 30622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 11622 35.39 - 70.78: 1287 70.78 - 106.16: 183 106.16 - 141.55: 15 141.55 - 176.94: 24 Dihedral angle restraints: 13131 sinusoidal: 8880 harmonic: 4251 Sorted by residual: dihedral pdb=" O4' U H 138 " pdb=" C1' U H 138 " pdb=" N1 U H 138 " pdb=" C2 U H 138 " ideal model delta sinusoidal sigma weight residual -160.00 -0.39 -159.61 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' U I 138 " pdb=" C1' U I 138 " pdb=" N1 U I 138 " pdb=" C2 U I 138 " ideal model delta sinusoidal sigma weight residual -160.00 -0.44 -159.56 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U G 138 " pdb=" C1' U G 138 " pdb=" N1 U G 138 " pdb=" C2 U G 138 " ideal model delta sinusoidal sigma weight residual -160.00 -0.45 -159.55 1 1.50e+01 4.44e-03 8.26e+01 ... (remaining 13128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2743 0.054 - 0.109: 662 0.109 - 0.163: 384 0.163 - 0.217: 36 0.217 - 0.272: 3 Chirality restraints: 3828 Sorted by residual: chirality pdb=" C3' U I 59 " pdb=" C4' U I 59 " pdb=" O3' U I 59 " pdb=" C2' U I 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' U H 59 " pdb=" C4' U H 59 " pdb=" O3' U H 59 " pdb=" C2' U H 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C3' U G 59 " pdb=" C4' U G 59 " pdb=" O3' U G 59 " pdb=" C2' U G 59 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 3825 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 448 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ASP B 448 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP B 448 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE B 449 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 448 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" C ASP A 448 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 448 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 449 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 448 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C ASP C 448 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP C 448 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE C 449 " 0.015 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5656 2.81 - 3.33: 16937 3.33 - 3.86: 36330 3.86 - 4.38: 40211 4.38 - 4.90: 59377 Nonbonded interactions: 158511 Sorted by model distance: nonbonded pdb=" O4' U H 138 " pdb=" O2 U H 138 " model vdw 2.291 3.040 nonbonded pdb=" O4' U G 138 " pdb=" O2 U G 138 " model vdw 2.292 3.040 nonbonded pdb=" O4' U I 138 " pdb=" O2 U I 138 " model vdw 2.293 3.040 nonbonded pdb=" OG SER C 383 " pdb=" O2' G I 58 " model vdw 2.314 3.040 nonbonded pdb=" OG SER A 383 " pdb=" O2' G G 58 " model vdw 2.314 3.040 ... (remaining 158506 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 10.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.880 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21075 Z= 0.297 Angle : 0.799 6.979 30627 Z= 0.661 Chirality : 0.060 0.272 3828 Planarity : 0.004 0.026 2313 Dihedral : 26.029 176.940 10377 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 15.07 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.22), residues: 1431 helix: 1.67 (0.20), residues: 771 sheet: -0.33 (0.47), residues: 120 loop : -0.58 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 385 TYR 0.012 0.001 TYR B 306 PHE 0.009 0.001 PHE C 440 TRP 0.008 0.001 TRP C 250 HIS 0.008 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.30 (21075) covalent geometry : angle 0.79864 / 0.66 (30627) hydrogen bonds : bond 0.17833 / 11.70 ( 738) hydrogen bonds : angle 5.31728 / 3.83 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.554 Fit side-chains outliers start: 16 outliers final: 3 residues processed: 71 average time/residue: 0.1572 time to fit residues: 17.4629 Evaluate side-chains 44 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0040 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.062552 restraints weight = 55159.138| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.81 r_work: 0.2783 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21075 Z= 0.152 Angle : 0.562 10.966 30627 Z= 0.317 Chirality : 0.043 0.544 3828 Planarity : 0.004 0.032 2313 Dihedral : 26.419 177.816 8172 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.44 % Allowed : 15.69 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1431 helix: 2.11 (0.19), residues: 780 sheet: 0.04 (0.47), residues: 117 loop : -0.53 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 385 TYR 0.019 0.002 TYR B 70 PHE 0.010 0.001 PHE C 440 TRP 0.012 0.001 TRP C 250 HIS 0.008 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (21075) covalent geometry : angle 0.56185 / 0.32 (30627) hydrogen bonds : bond 0.07804 / 5.09 ( 738) hydrogen bonds : angle 3.95772 / 2.87 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.601 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 0.1191 time to fit residues: 12.6256 Evaluate side-chains 57 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 265 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 54 optimal weight: 30.0000 chunk 140 optimal weight: 0.0060 chunk 135 optimal weight: 0.0470 chunk 183 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.4894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.098417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065052 restraints weight = 55809.998| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.82 r_work: 0.2822 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21075 Z= 0.109 Angle : 0.477 10.679 30627 Z= 0.272 Chirality : 0.039 0.389 3828 Planarity : 0.003 0.019 2313 Dihedral : 26.045 179.405 8168 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.83 % Allowed : 15.07 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1431 helix: 2.55 (0.19), residues: 786 sheet: 0.31 (0.47), residues: 117 loop : -0.43 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.016 0.001 TYR B 70 PHE 0.010 0.001 PHE A 120 TRP 0.008 0.001 TRP C 250 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (21075) covalent geometry : angle 0.47675 / 0.27 (30627) hydrogen bonds : bond 0.06596 / 4.34 ( 738) hydrogen bonds : angle 3.54109 / 2.56 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.547 Fit side-chains REVERT: A 60 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8132 (mtmt) REVERT: A 166 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8294 (mt-10) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.1178 time to fit residues: 11.5107 Evaluate side-chains 49 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 156 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 135 optimal weight: 0.0020 chunk 179 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.097556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.062802 restraints weight = 55491.168| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.80 r_work: 0.2796 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21075 Z= 0.120 Angle : 0.489 10.738 30627 Z= 0.273 Chirality : 0.039 0.480 3828 Planarity : 0.003 0.019 2313 Dihedral : 25.739 178.732 8166 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.86 % Allowed : 13.73 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.23), residues: 1431 helix: 2.71 (0.19), residues: 786 sheet: 0.48 (0.46), residues: 117 loop : -0.46 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.017 0.001 TYR C 329 PHE 0.011 0.001 PHE B 120 TRP 0.011 0.001 TRP C 250 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (21075) covalent geometry : angle 0.48864 / 0.27 (30627) hydrogen bonds : bond 0.06993 / 4.63 ( 738) hydrogen bonds : angle 3.41717 / 2.47 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.480 Fit side-chains REVERT: A 60 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8146 (mtmt) REVERT: A 166 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8283 (mt-10) REVERT: C 60 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8645 (mtmm) outliers start: 18 outliers final: 11 residues processed: 62 average time/residue: 0.1345 time to fit residues: 13.9494 Evaluate side-chains 65 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.097940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.063468 restraints weight = 55290.446| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.78 r_work: 0.2812 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21075 Z= 0.102 Angle : 0.457 10.238 30627 Z= 0.258 Chirality : 0.037 0.416 3828 Planarity : 0.003 0.020 2313 Dihedral : 25.569 178.413 8166 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.24 % Allowed : 14.14 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.23), residues: 1431 helix: 2.84 (0.19), residues: 786 sheet: 0.59 (0.46), residues: 117 loop : -0.44 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 75 TYR 0.013 0.001 TYR B 329 PHE 0.011 0.001 PHE A 120 TRP 0.009 0.001 TRP A 250 HIS 0.007 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (21075) covalent geometry : angle 0.45676 / 0.26 (30627) hydrogen bonds : bond 0.06607 / 4.38 ( 738) hydrogen bonds : angle 3.33514 / 2.41 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.578 Fit side-chains REVERT: A 60 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8128 (mtmt) REVERT: A 166 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8265 (mt-10) outliers start: 12 outliers final: 11 residues processed: 60 average time/residue: 0.1135 time to fit residues: 12.1891 Evaluate side-chains 54 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 57 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 143 optimal weight: 0.0070 chunk 132 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062782 restraints weight = 55577.879| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.80 r_work: 0.2792 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21075 Z= 0.113 Angle : 0.466 8.294 30627 Z= 0.261 Chirality : 0.037 0.427 3828 Planarity : 0.003 0.020 2313 Dihedral : 25.309 177.872 8166 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.75 % Allowed : 13.52 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.23), residues: 1431 helix: 2.89 (0.19), residues: 786 sheet: 0.63 (0.46), residues: 117 loop : -0.38 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 75 TYR 0.014 0.001 TYR C 329 PHE 0.011 0.001 PHE B 120 TRP 0.010 0.001 TRP A 250 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (21075) covalent geometry : angle 0.46589 / 0.26 (30627) hydrogen bonds : bond 0.06769 / 4.51 ( 738) hydrogen bonds : angle 3.27911 / 2.37 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.565 Fit side-chains REVERT: A 60 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8143 (mtmt) REVERT: A 166 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8288 (mt-10) outliers start: 17 outliers final: 14 residues processed: 62 average time/residue: 0.1138 time to fit residues: 12.2724 Evaluate side-chains 60 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 177 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 176 optimal weight: 40.0000 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062122 restraints weight = 55770.309| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.81 r_work: 0.2776 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21075 Z= 0.119 Angle : 0.460 7.534 30627 Z= 0.259 Chirality : 0.037 0.400 3828 Planarity : 0.003 0.021 2313 Dihedral : 25.186 177.768 8166 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.24 % Allowed : 14.24 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.23), residues: 1431 helix: 2.95 (0.19), residues: 786 sheet: 0.70 (0.46), residues: 117 loop : -0.37 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 385 TYR 0.015 0.001 TYR B 329 PHE 0.013 0.001 PHE A 120 TRP 0.008 0.001 TRP B 250 HIS 0.006 0.001 HIS C 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (21075) covalent geometry : angle 0.46036 / 0.26 (30627) hydrogen bonds : bond 0.07119 / 4.75 ( 738) hydrogen bonds : angle 3.34544 / 2.41 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.576 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.1146 time to fit residues: 12.1122 Evaluate side-chains 53 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.097557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.062639 restraints weight = 55660.786| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.81 r_work: 0.2789 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21075 Z= 0.105 Angle : 0.448 6.650 30627 Z= 0.253 Chirality : 0.036 0.409 3828 Planarity : 0.003 0.020 2313 Dihedral : 25.122 177.837 8166 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.55 % Allowed : 14.65 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.23), residues: 1431 helix: 2.97 (0.19), residues: 786 sheet: 0.77 (0.47), residues: 117 loop : -0.36 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.013 0.001 TYR C 329 PHE 0.012 0.001 PHE A 120 TRP 0.009 0.001 TRP C 250 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.11 (21075) covalent geometry : angle 0.44767 / 0.25 (30627) hydrogen bonds : bond 0.06708 / 4.48 ( 738) hydrogen bonds : angle 3.26164 / 2.35 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.533 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 56 average time/residue: 0.1079 time to fit residues: 10.6630 Evaluate side-chains 55 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 101 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.062565 restraints weight = 55455.605| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.79 r_work: 0.2786 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21075 Z= 0.109 Angle : 0.448 6.688 30627 Z= 0.254 Chirality : 0.037 0.389 3828 Planarity : 0.003 0.021 2313 Dihedral : 24.972 178.828 8166 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.55 % Allowed : 14.34 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.23), residues: 1431 helix: 3.02 (0.19), residues: 786 sheet: 0.76 (0.47), residues: 117 loop : -0.35 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 385 TYR 0.015 0.001 TYR B 329 PHE 0.013 0.001 PHE A 120 TRP 0.008 0.001 TRP C 250 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (21075) covalent geometry : angle 0.44840 / 0.25 (30627) hydrogen bonds : bond 0.06820 / 4.58 ( 738) hydrogen bonds : angle 3.27954 / 2.36 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.542 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 58 average time/residue: 0.0966 time to fit residues: 9.8495 Evaluate side-chains 54 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 15 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.096732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066228 restraints weight = 55869.476| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.24 r_work: 0.2691 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21075 Z= 0.131 Angle : 0.464 6.702 30627 Z= 0.261 Chirality : 0.038 0.410 3828 Planarity : 0.003 0.023 2313 Dihedral : 24.948 179.014 8166 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.34 % Allowed : 14.76 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.23), residues: 1431 helix: 2.97 (0.19), residues: 783 sheet: 0.76 (0.47), residues: 117 loop : -0.39 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 131 TYR 0.015 0.001 TYR B 329 PHE 0.012 0.001 PHE C 120 TRP 0.010 0.001 TRP C 250 HIS 0.007 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (21075) covalent geometry : angle 0.46384 / 0.26 (30627) hydrogen bonds : bond 0.07404 / 4.95 ( 738) hydrogen bonds : angle 3.37591 / 2.43 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.560 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 57 average time/residue: 0.0907 time to fit residues: 9.3955 Evaluate side-chains 56 residues out of total 1317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 163 optimal weight: 0.7980 chunk 158 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 166 optimal weight: 0.0980 chunk 5 optimal weight: 0.0000 chunk 14 optimal weight: 0.4980 chunk 122 optimal weight: 10.0000 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.098766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.064129 restraints weight = 56242.058| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.81 r_work: 0.2825 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21075 Z= 0.091 Angle : 0.427 6.218 30627 Z= 0.244 Chirality : 0.035 0.384 3828 Planarity : 0.003 0.020 2313 Dihedral : 24.894 179.565 8166 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.55 % Allowed : 14.65 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.23), residues: 1431 helix: 3.09 (0.19), residues: 786 sheet: 0.89 (0.48), residues: 117 loop : -0.33 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 123 TYR 0.011 0.001 TYR B 329 PHE 0.013 0.001 PHE A 120 TRP 0.008 0.001 TRP B 250 HIS 0.006 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.09 (21075) covalent geometry : angle 0.42663 / 0.24 (30627) hydrogen bonds : bond 0.06040 / 4.08 ( 738) hydrogen bonds : angle 3.16320 / 2.28 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.21 seconds wall clock time: 79 minutes 3.40 seconds (4743.40 seconds total)