Starting phenix.real_space_refine on Fri Jul 25 15:22:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.map" model { file = "/net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yot_39457/07_2025/8yot_39457.cif" } resolution = 2.48 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= -0.002 sd= 0.160 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 4908 2.51 5 N 1338 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7738 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 110} Chain: "B" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2990 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 879 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2990 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 350} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Residues with excluded nonbonded symmetry interactions: 45 residue: pdb=" N GLN A 25 " occ=0.55 ... (7 atoms not shown) pdb=" NE2 GLN A 25 " occ=0.33 residue: pdb=" N SER A 29 " occ=0.71 ... (4 atoms not shown) pdb=" OG SER A 29 " occ=0.00 residue: pdb=" N GLY A 31 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY A 31 " occ=0.29 residue: pdb=" N GLY A 32 " occ=0.84 ... (2 atoms not shown) pdb=" O GLY A 32 " occ=0.56 residue: pdb=" N VAL A 34 " occ=0.51 ... (5 atoms not shown) pdb=" CG2 VAL A 34 " occ=0.00 residue: pdb=" N GLN A 35 " occ=0.23 ... (7 atoms not shown) pdb=" NE2 GLN A 35 " occ=0.40 residue: pdb=" N ALA A 36 " occ=0.37 ... (3 atoms not shown) pdb=" CB ALA A 36 " occ=0.82 residue: pdb=" N GLY A 37 " occ=0.11 ... (2 atoms not shown) pdb=" O GLY A 37 " occ=0.69 residue: pdb=" N GLY A 38 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 38 " occ=0.10 residue: pdb=" N SER A 39 " occ=0.65 ... (4 atoms not shown) pdb=" OG SER A 39 " occ=0.00 residue: pdb=" N SER A 49 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 49 " occ=0.31 residue: pdb=" N ILE A 50 " occ=0.94 ... (6 atoms not shown) pdb=" CD1 ILE A 50 " occ=0.79 ... (remaining 33 not shown) Time building chain proxies: 5.36, per 1000 atoms: 0.69 Number of scatterers: 7738 At special positions: 0 Unit cell: (115.28, 135.042, 81.2446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1450 8.00 N 1338 7.00 C 4908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 245 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 345 " - pdb=" SG CYS B 396 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 245 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 396 " distance=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 28 sheets defined 3.8% alpha, 52.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.606A pdb=" N LYS A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.647A pdb=" N HIS B 390 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 391' Processing helix chain 'C' and resid 83 through 86 removed outlier: 3.590A pdb=" N LYS C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 86' Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'D' and resid 287 through 291 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.604A pdb=" N HIS D 390 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 5.760A pdb=" N PHE A 69 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG A 60 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 81 removed outlier: 5.760A pdb=" N PHE A 69 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG A 60 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 33 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 40 removed outlier: 4.184A pdb=" N GLU B 57 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.554A pdb=" N GLY B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 125 through 128 Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.635A pdb=" N VAL B 134 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 152 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.635A pdb=" N VAL B 134 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TRP B 192 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N CYS B 196 " --> pdb=" O TRP B 207 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N TRP B 207 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N TYR B 198 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLN B 205 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR B 200 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 226 through 229 removed outlier: 5.773A pdb=" N LEU B 241 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB3, first strand: chain 'B' and resid 234 through 235 removed outlier: 7.638A pdb=" N LEU B 407 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N MET B 317 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB5, first strand: chain 'B' and resid 334 through 336 Processing sheet with id=AB6, first strand: chain 'C' and resid 26 through 29 Processing sheet with id=AB7, first strand: chain 'C' and resid 79 through 81 removed outlier: 7.058A pdb=" N ARG C 67 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ALA C 62 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE C 69 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG C 60 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 114 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 79 through 81 removed outlier: 7.058A pdb=" N ARG C 67 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ALA C 62 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE C 69 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG C 60 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL C 114 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 40 removed outlier: 4.133A pdb=" N GLU D 57 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 40 Processing sheet with id=AC3, first strand: chain 'D' and resid 125 through 128 Processing sheet with id=AC4, first strand: chain 'D' and resid 133 through 135 removed outlier: 6.631A pdb=" N VAL D 134 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D 152 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 133 through 135 removed outlier: 6.631A pdb=" N VAL D 134 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP D 192 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N CYS D 196 " --> pdb=" O TRP D 207 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N TRP D 207 " --> pdb=" O CYS D 196 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N TYR D 198 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN D 205 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR D 200 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 226 through 229 removed outlier: 5.754A pdb=" N LEU D 241 " --> pdb=" O LEU D 283 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC8, first strand: chain 'D' and resid 234 through 235 removed outlier: 7.648A pdb=" N LEU D 407 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET D 317 " --> pdb=" O LEU D 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 326 through 329 Processing sheet with id=AD1, first strand: chain 'D' and resid 334 through 336 removed outlier: 3.518A pdb=" N GLY D 392 " --> pdb=" O LEU D 416 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2509 1.35 - 1.47: 2055 1.47 - 1.59: 3344 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 7972 Sorted by residual: bond pdb=" CB GLN C 132 " pdb=" CG GLN C 132 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CG GLN C 132 " pdb=" CD GLN C 132 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.76e-01 bond pdb=" N PRO D 364 " pdb=" CA PRO D 364 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 7.53e-01 bond pdb=" N PRO B 364 " pdb=" CA PRO B 364 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.57e-01 bond pdb=" C GLN B 330 " pdb=" N PRO B 331 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.50e-01 ... (remaining 7967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 10682 2.08 - 4.16: 156 4.16 - 6.24: 11 6.24 - 8.33: 3 8.33 - 10.41: 2 Bond angle restraints: 10854 Sorted by residual: angle pdb=" N ARG C 88 " pdb=" CA ARG C 88 " pdb=" C ARG C 88 " ideal model delta sigma weight residual 114.04 109.86 4.18 1.24e+00 6.50e-01 1.14e+01 angle pdb=" N ARG A 88 " pdb=" CA ARG A 88 " pdb=" C ARG A 88 " ideal model delta sigma weight residual 114.04 110.27 3.77 1.24e+00 6.50e-01 9.23e+00 angle pdb=" CA LEU D 53 " pdb=" CB LEU D 53 " pdb=" CG LEU D 53 " ideal model delta sigma weight residual 116.30 126.71 -10.41 3.50e+00 8.16e-02 8.84e+00 angle pdb=" CA CYS B 144 " pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " ideal model delta sigma weight residual 114.40 120.97 -6.57 2.30e+00 1.89e-01 8.16e+00 angle pdb=" CA CYS D 144 " pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " ideal model delta sigma weight residual 114.40 120.96 -6.56 2.30e+00 1.89e-01 8.13e+00 ... (remaining 10849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4265 17.03 - 34.06: 323 34.06 - 51.09: 84 51.09 - 68.12: 21 68.12 - 85.15: 11 Dihedral angle restraints: 4704 sinusoidal: 1840 harmonic: 2864 Sorted by residual: dihedral pdb=" CB CYS D 245 " pdb=" SG CYS D 245 " pdb=" SG CYS D 296 " pdb=" CB CYS D 296 " ideal model delta sinusoidal sigma weight residual -86.00 -160.03 74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS B 245 " pdb=" SG CYS B 245 " pdb=" SG CYS B 296 " pdb=" CB CYS B 296 " ideal model delta sinusoidal sigma weight residual -86.00 -158.93 72.93 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CA SER D 136 " pdb=" C SER D 136 " pdb=" N GLY D 137 " pdb=" CA GLY D 137 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 645 0.028 - 0.056: 330 0.056 - 0.084: 69 0.084 - 0.112: 71 0.112 - 0.140: 17 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CA LEU B 129 " pdb=" N LEU B 129 " pdb=" C LEU B 129 " pdb=" CB LEU B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA LEU D 129 " pdb=" N LEU D 129 " pdb=" C LEU D 129 " pdb=" CB LEU D 129 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE D 321 " pdb=" N ILE D 321 " pdb=" C ILE D 321 " pdb=" CB ILE D 321 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1129 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 115 " -0.007 2.00e-02 2.50e+03 7.30e-03 1.07e+00 pdb=" CG TYR A 115 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 115 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 115 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 115 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 115 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 115 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 53 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C LEU D 53 " -0.018 2.00e-02 2.50e+03 pdb=" O LEU D 53 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU D 54 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 62 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 63 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 63 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 63 " -0.014 5.00e-02 4.00e+02 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1690 2.79 - 3.32: 6123 3.32 - 3.84: 12778 3.84 - 4.37: 15529 4.37 - 4.90: 26056 Nonbonded interactions: 62176 Sorted by model distance: nonbonded pdb=" NH2 ARG B 253 " pdb=" O SER B 303 " model vdw 2.258 3.120 nonbonded pdb=" OG SER D 222 " pdb=" OH TYR D 251 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG D 253 " pdb=" O SER D 303 " model vdw 2.269 3.120 nonbonded pdb=" OG SER B 222 " pdb=" OH TYR B 251 " model vdw 2.281 3.040 nonbonded pdb=" NE2 GLN D 244 " pdb=" OE1 GLN D 278 " model vdw 2.294 3.120 ... (remaining 62171 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 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: 1.430 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.230 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.028 7982 Z= 0.145 Angle : 0.637 10.407 10874 Z= 0.337 Chirality : 0.041 0.140 1132 Planarity : 0.004 0.025 1416 Dihedral : 14.052 85.150 2862 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.08 % Allowed : 13.98 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.06 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.80 (0.25), residues: 434 loop : -0.58 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS B 151 PHE 0.012 0.002 PHE B 177 TYR 0.018 0.002 TYR A 115 ARG 0.003 0.000 ARG D 95 Details of bonding type rmsd hydrogen bonds : bond 0.22516 ( 285) hydrogen bonds : angle 8.67487 ( 762) SS BOND : bond 0.00241 ( 10) SS BOND : angle 2.15156 ( 20) covalent geometry : bond 0.00314 ( 7972) covalent geometry : angle 0.63060 (10854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.737 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.9506 time to fit residues: 103.3409 Evaluate side-chains 95 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 383 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 HIS B 152 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.172790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126862 restraints weight = 6735.185| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.78 r_work: 0.3131 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 169 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 152 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7982 Z= 0.246 Angle : 0.742 10.978 10874 Z= 0.380 Chirality : 0.048 0.175 1132 Planarity : 0.005 0.036 1416 Dihedral : 6.034 58.251 1108 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.22 % Allowed : 12.05 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.05 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.78 (0.25), residues: 440 loop : -0.59 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 348 HIS 0.005 0.001 HIS B 151 PHE 0.017 0.003 PHE B 177 TYR 0.019 0.003 TYR D 96 ARG 0.005 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 285) hydrogen bonds : angle 5.94206 ( 762) SS BOND : bond 0.00385 ( 10) SS BOND : angle 2.56370 ( 20) covalent geometry : bond 0.00574 ( 7972) covalent geometry : angle 0.73426 (10854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.834 Fit side-chains REVERT: D 270 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7359 (mm-40) REVERT: D 369 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7089 (mtt-85) outliers start: 35 outliers final: 20 residues processed: 121 average time/residue: 0.9525 time to fit residues: 123.8032 Evaluate side-chains 113 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 369 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130715 restraints weight = 6757.460| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.70 r_work: 0.3175 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 152 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7982 Z= 0.116 Angle : 0.585 8.810 10874 Z= 0.300 Chirality : 0.042 0.134 1132 Planarity : 0.004 0.029 1416 Dihedral : 4.942 33.350 1101 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.73 % Allowed : 12.77 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.90 (0.25), residues: 446 loop : -0.43 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 348 HIS 0.005 0.001 HIS B 152 PHE 0.010 0.002 PHE B 281 TYR 0.013 0.002 TYR B 197 ARG 0.002 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 285) hydrogen bonds : angle 5.33173 ( 762) SS BOND : bond 0.00289 ( 10) SS BOND : angle 1.88735 ( 20) covalent geometry : bond 0.00269 ( 7972) covalent geometry : angle 0.58036 (10854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.898 Fit side-chains REVERT: A 68 GLU cc_start: 0.8116 (pt0) cc_final: 0.7902 (pt0) REVERT: A 101 TYR cc_start: 0.8177 (m-80) cc_final: 0.7935 (m-80) REVERT: B 369 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7317 (mtt-85) REVERT: D 371 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7486 (mmt) outliers start: 31 outliers final: 16 residues processed: 113 average time/residue: 1.1785 time to fit residues: 143.1754 Evaluate side-chains 108 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 371 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.173804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127335 restraints weight = 6730.039| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.76 r_work: 0.3128 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 161 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 162 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7982 Z= 0.183 Angle : 0.659 9.780 10874 Z= 0.334 Chirality : 0.044 0.157 1132 Planarity : 0.005 0.032 1416 Dihedral : 5.236 33.448 1101 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.46 % Allowed : 12.05 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.23 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.91 (0.25), residues: 446 loop : -0.48 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 306 HIS 0.004 0.001 HIS B 405 PHE 0.013 0.002 PHE D 177 TYR 0.015 0.002 TYR B 257 ARG 0.004 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 285) hydrogen bonds : angle 5.21742 ( 762) SS BOND : bond 0.00360 ( 10) SS BOND : angle 2.39467 ( 20) covalent geometry : bond 0.00429 ( 7972) covalent geometry : angle 0.65128 (10854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.758 Fit side-chains REVERT: B 97 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6971 (mtm-85) REVERT: B 270 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: D 369 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7058 (mtt-85) REVERT: D 371 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7398 (mmt) REVERT: D 378 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8573 (pm20) outliers start: 37 outliers final: 15 residues processed: 118 average time/residue: 0.9415 time to fit residues: 119.6007 Evaluate side-chains 111 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 378 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 239 GLN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN D 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127698 restraints weight = 6666.107| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.76 r_work: 0.3138 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 162 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 162 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7982 Z= 0.227 Angle : 0.720 12.890 10874 Z= 0.362 Chirality : 0.047 0.175 1132 Planarity : 0.005 0.036 1416 Dihedral : 5.538 33.378 1101 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.70 % Allowed : 12.77 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.16 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.85 (0.25), residues: 442 loop : -0.51 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 348 HIS 0.004 0.001 HIS D 92 PHE 0.016 0.003 PHE D 177 TYR 0.018 0.003 TYR B 96 ARG 0.005 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 285) hydrogen bonds : angle 5.20761 ( 762) SS BOND : bond 0.00396 ( 10) SS BOND : angle 2.67132 ( 20) covalent geometry : bond 0.00531 ( 7972) covalent geometry : angle 0.71179 (10854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.791 Fit side-chains REVERT: A 104 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: B 270 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: B 369 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7083 (mtt-85) REVERT: C 40 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7902 (mt) REVERT: D 369 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7008 (mtt-85) REVERT: D 371 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7397 (mmt) REVERT: D 378 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8642 (pm20) outliers start: 39 outliers final: 21 residues processed: 114 average time/residue: 1.3163 time to fit residues: 160.2011 Evaluate side-chains 119 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 270 GLN Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 378 GLN Chi-restraints excluded: chain D residue 383 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128966 restraints weight = 6647.736| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.78 r_work: 0.3156 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 162 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 163 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7982 Z= 0.126 Angle : 0.599 11.050 10874 Z= 0.303 Chirality : 0.042 0.130 1132 Planarity : 0.004 0.032 1416 Dihedral : 5.075 33.064 1101 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.34 % Allowed : 13.13 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.33 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.90 (0.25), residues: 448 loop : -0.34 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 348 HIS 0.003 0.001 HIS D 151 PHE 0.010 0.002 PHE B 281 TYR 0.014 0.002 TYR B 197 ARG 0.002 0.000 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 285) hydrogen bonds : angle 4.97471 ( 762) SS BOND : bond 0.00293 ( 10) SS BOND : angle 2.00913 ( 20) covalent geometry : bond 0.00294 ( 7972) covalent geometry : angle 0.59310 (10854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.934 Fit side-chains REVERT: A 104 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: B 369 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7196 (mtt-85) REVERT: C 40 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7766 (mt) REVERT: D 369 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7028 (mtt-85) REVERT: D 378 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8614 (pm20) outliers start: 36 outliers final: 19 residues processed: 114 average time/residue: 1.0640 time to fit residues: 130.6830 Evaluate side-chains 117 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 378 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN D 122 ASN D 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129788 restraints weight = 6731.433| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.81 r_work: 0.3167 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 163 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7982 Z= 0.112 Angle : 0.586 11.311 10874 Z= 0.294 Chirality : 0.042 0.132 1132 Planarity : 0.004 0.030 1416 Dihedral : 4.895 32.917 1101 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.25 % Allowed : 14.22 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.36 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.93 (0.25), residues: 446 loop : -0.33 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 348 HIS 0.002 0.001 HIS D 151 PHE 0.009 0.002 PHE B 281 TYR 0.015 0.001 TYR D 197 ARG 0.002 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 285) hydrogen bonds : angle 4.86687 ( 762) SS BOND : bond 0.00277 ( 10) SS BOND : angle 2.13769 ( 20) covalent geometry : bond 0.00263 ( 7972) covalent geometry : angle 0.57893 (10854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.625 Fit side-chains REVERT: A 40 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7623 (mt) REVERT: A 101 TYR cc_start: 0.8093 (m-80) cc_final: 0.7848 (m-80) REVERT: A 104 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: B 369 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7187 (mtt-85) REVERT: C 40 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 66 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: D 369 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7002 (mtt-85) outliers start: 27 outliers final: 18 residues processed: 109 average time/residue: 1.3005 time to fit residues: 153.8943 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 369 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN D 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129563 restraints weight = 6745.738| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.81 r_work: 0.3162 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 167 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7982 Z= 0.122 Angle : 0.585 10.837 10874 Z= 0.294 Chirality : 0.042 0.136 1132 Planarity : 0.004 0.031 1416 Dihedral : 4.853 32.930 1100 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.25 % Allowed : 14.46 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.40 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.98 (0.25), residues: 446 loop : -0.32 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.003 0.001 HIS B 405 PHE 0.009 0.002 PHE B 281 TYR 0.014 0.002 TYR B 197 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 285) hydrogen bonds : angle 4.79851 ( 762) SS BOND : bond 0.00299 ( 10) SS BOND : angle 1.98780 ( 20) covalent geometry : bond 0.00287 ( 7972) covalent geometry : angle 0.57948 (10854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.796 Fit side-chains REVERT: A 47 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7403 (p) REVERT: A 104 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7638 (mtp) REVERT: B 369 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7188 (mtt-85) REVERT: C 40 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7737 (mt) REVERT: C 66 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: D 369 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7029 (mtt-85) outliers start: 27 outliers final: 19 residues processed: 106 average time/residue: 0.8866 time to fit residues: 101.6636 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 369 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN D 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.174977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128246 restraints weight = 6825.520| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.79 r_work: 0.3137 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7982 Z= 0.157 Angle : 0.626 10.685 10874 Z= 0.315 Chirality : 0.043 0.150 1132 Planarity : 0.004 0.032 1416 Dihedral : 5.058 33.265 1100 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 14.22 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.35 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.92 (0.25), residues: 450 loop : -0.34 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 306 HIS 0.003 0.001 HIS B 405 PHE 0.011 0.002 PHE D 177 TYR 0.013 0.002 TYR B 197 ARG 0.003 0.000 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 285) hydrogen bonds : angle 4.81058 ( 762) SS BOND : bond 0.00352 ( 10) SS BOND : angle 2.28093 ( 20) covalent geometry : bond 0.00369 ( 7972) covalent geometry : angle 0.61903 (10854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.908 Fit side-chains REVERT: A 40 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 104 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7690 (mtp) REVERT: B 369 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7131 (mtt-85) REVERT: C 40 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7763 (mt) REVERT: C 104 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7768 (mtp) REVERT: D 369 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7017 (mtt-85) outliers start: 29 outliers final: 17 residues processed: 107 average time/residue: 0.9739 time to fit residues: 112.2169 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 369 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN D 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129762 restraints weight = 6817.637| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.82 r_work: 0.3170 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 170 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7982 Z= 0.114 Angle : 0.570 11.099 10874 Z= 0.288 Chirality : 0.042 0.125 1132 Planarity : 0.004 0.032 1416 Dihedral : 4.808 32.816 1100 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.13 % Allowed : 14.46 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.45 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.96 (0.25), residues: 452 loop : -0.24 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 306 HIS 0.003 0.001 HIS B 151 PHE 0.009 0.002 PHE B 281 TYR 0.011 0.002 TYR B 397 ARG 0.002 0.000 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 285) hydrogen bonds : angle 4.70585 ( 762) SS BOND : bond 0.00293 ( 10) SS BOND : angle 1.62617 ( 20) covalent geometry : bond 0.00269 ( 7972) covalent geometry : angle 0.56614 (10854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.879 Fit side-chains REVERT: A 40 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 47 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.7379 (p) REVERT: A 98 ASN cc_start: 0.6994 (m-40) cc_final: 0.6658 (m110) REVERT: A 104 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7594 (mtp) REVERT: B 369 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7183 (mtt-85) REVERT: C 40 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7751 (mt) REVERT: C 66 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: C 104 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: D 369 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6974 (mtt-85) outliers start: 26 outliers final: 16 residues processed: 106 average time/residue: 0.9244 time to fit residues: 105.8513 Evaluate side-chains 115 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 369 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.177512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131263 restraints weight = 6749.430| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.80 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 170 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 172 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7982 Z= 0.099 Angle : 0.552 10.929 10874 Z= 0.277 Chirality : 0.041 0.126 1132 Planarity : 0.004 0.031 1416 Dihedral : 4.645 32.586 1100 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 15.42 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.50 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.95 (0.25), residues: 452 loop : -0.17 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 306 HIS 0.003 0.001 HIS B 152 PHE 0.009 0.001 PHE B 281 TYR 0.012 0.001 TYR C 116 ARG 0.002 0.000 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 285) hydrogen bonds : angle 4.61914 ( 762) SS BOND : bond 0.00297 ( 10) SS BOND : angle 1.63694 ( 20) covalent geometry : bond 0.00235 ( 7972) covalent geometry : angle 0.54776 (10854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7732.22 seconds wall clock time: 137 minutes 21.72 seconds (8241.72 seconds total)