Starting phenix.real_space_refine on Wed Sep 17 09:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yot_39457/09_2025/8yot_39457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yot_39457/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yot_39457/09_2025/8yot_39457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yot_39457/09_2025/8yot_39457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yot_39457/09_2025/8yot_39457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yot_39457/09_2025/8yot_39457.map" } resolution = 2.48 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= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 1, 'ARG: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, 'ASP:plan': 1, 'ARG: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: 2.01, per 1000 atoms: 0.26 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: 0.53 Conformation dependent library (CDL) restraints added in 412.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.44 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: 1.47 Time building geometry restraints manager: 0.75 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: 0.00 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG D 95 TYR 0.018 0.002 TYR A 115 PHE 0.012 0.002 PHE B 177 TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7972) covalent geometry : angle 0.63060 (10854) SS BOND : bond 0.00241 ( 10) SS BOND : angle 2.15156 ( 20) hydrogen bonds : bond 0.22516 ( 285) hydrogen bonds : angle 8.67487 ( 762) *********************** 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 : 0.327 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.4854 time to fit residues: 52.7222 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 : 0.295 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.126494 restraints weight = 6793.129| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.80 r_work: 0.3123 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 169 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7982 Z= 0.256 Angle : 0.754 11.061 10874 Z= 0.387 Chirality : 0.048 0.177 1132 Planarity : 0.006 0.038 1416 Dihedral : 6.081 58.724 1108 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.34 % Allowed : 11.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.78 (0.25), residues: 440 loop : -0.60 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 288 TYR 0.020 0.003 TYR D 96 PHE 0.018 0.003 PHE B 177 TRP 0.014 0.003 TRP B 348 HIS 0.005 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00597 ( 7972) covalent geometry : angle 0.74698 (10854) SS BOND : bond 0.00368 ( 10) SS BOND : angle 2.58561 ( 20) hydrogen bonds : bond 0.04655 ( 285) hydrogen bonds : angle 5.91216 ( 762) *********************** 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 132 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.370 Fit side-chains REVERT: D 270 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7351 (mm-40) REVERT: D 369 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7116 (mtt-85) outliers start: 36 outliers final: 21 residues processed: 122 average time/residue: 0.4872 time to fit residues: 63.6875 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 : 0.333 ------------------------------------------------------------------------------- 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 357 THR 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 42 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 60 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128484 restraints weight = 6681.579| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.82 r_work: 0.3147 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 154 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1035 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= 0.134 Angle : 0.608 8.784 10874 Z= 0.312 Chirality : 0.043 0.134 1132 Planarity : 0.004 0.031 1416 Dihedral : 5.130 33.344 1102 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.86 % Allowed : 12.89 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.22 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.88 (0.25), residues: 446 loop : -0.47 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 88 TYR 0.012 0.002 TYR B 197 PHE 0.010 0.002 PHE B 281 TRP 0.010 0.001 TRP D 306 HIS 0.004 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7972) covalent geometry : angle 0.60208 (10854) SS BOND : bond 0.00291 ( 10) SS BOND : angle 2.03473 ( 20) hydrogen bonds : bond 0.03803 ( 285) hydrogen bonds : angle 5.37072 ( 762) *********************** 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 126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.306 Fit side-chains REVERT: C 116 TYR cc_start: 0.8667 (m-80) cc_final: 0.8464 (m-80) REVERT: D 270 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: D 371 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7509 (mmt) outliers start: 32 outliers final: 19 residues processed: 112 average time/residue: 0.4897 time to fit residues: 58.7686 Evaluate side-chains 110 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 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 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 30 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN 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 = 0.3948 r_free = 0.3948 target = 0.173977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128016 restraints weight = 6779.973| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.70 r_work: 0.3145 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 154 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 155 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7982 Z= 0.179 Angle : 0.656 9.737 10874 Z= 0.333 Chirality : 0.044 0.155 1132 Planarity : 0.005 0.032 1416 Dihedral : 5.274 33.432 1101 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.82 % Allowed : 11.93 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.21 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.89 (0.25), residues: 446 loop : -0.48 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.015 0.002 TYR D 257 PHE 0.013 0.002 PHE D 177 TRP 0.011 0.002 TRP B 306 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7972) covalent geometry : angle 0.64869 (10854) SS BOND : bond 0.00357 ( 10) SS BOND : angle 2.40283 ( 20) hydrogen bonds : bond 0.03795 ( 285) hydrogen bonds : angle 5.22225 ( 762) *********************** 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 128 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.346 Fit side-chains REVERT: B 369 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7116 (mtt-85) REVERT: D 270 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: D 369 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7084 (mtt-85) REVERT: D 371 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7438 (mmt) REVERT: D 378 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8622 (pm20) outliers start: 40 outliers final: 19 residues processed: 113 average time/residue: 0.4898 time to fit residues: 59.3607 Evaluate side-chains 113 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 369 ARG 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 201 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 270 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127691 restraints weight = 6781.629| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.76 r_work: 0.3130 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 155 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 156 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7982 Z= 0.168 Angle : 0.650 12.548 10874 Z= 0.327 Chirality : 0.044 0.149 1132 Planarity : 0.004 0.032 1416 Dihedral : 5.238 33.199 1101 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.18 % Allowed : 12.17 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.25 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.90 (0.25), residues: 446 loop : -0.45 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.014 0.002 TYR B 257 PHE 0.012 0.002 PHE D 177 TRP 0.011 0.002 TRP B 306 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 7972) covalent geometry : angle 0.64321 (10854) SS BOND : bond 0.00338 ( 10) SS BOND : angle 2.27423 ( 20) hydrogen bonds : bond 0.03616 ( 285) hydrogen bonds : angle 5.08717 ( 762) *********************** 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 137 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 0.311 Fit side-chains REVERT: A 104 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7655 (mtp) REVERT: B 369 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7151 (mtt-85) REVERT: D 270 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: D 369 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7047 (mtt-85) REVERT: D 371 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7382 (mmt) REVERT: D 378 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8635 (pm20) outliers start: 43 outliers final: 24 residues processed: 118 average time/residue: 0.4823 time to fit residues: 61.1573 Evaluate side-chains 123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 287 SER Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 369 ARG 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 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 201 MET Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 270 GLN 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 64 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 ASN D 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.174461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128888 restraints weight = 6754.329| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.72 r_work: 0.3145 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 156 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 159 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7982 Z= 0.192 Angle : 0.675 10.807 10874 Z= 0.341 Chirality : 0.045 0.164 1132 Planarity : 0.005 0.034 1416 Dihedral : 5.391 33.408 1101 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.58 % Allowed : 12.65 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.22 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.88 (0.25), residues: 446 loop : -0.46 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 288 TYR 0.015 0.002 TYR D 257 PHE 0.014 0.002 PHE D 177 TRP 0.012 0.002 TRP D 306 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 7972) covalent geometry : angle 0.66687 (10854) SS BOND : bond 0.00371 ( 10) SS BOND : angle 2.46957 ( 20) hydrogen bonds : bond 0.03728 ( 285) hydrogen bonds : angle 5.08710 ( 762) *********************** 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 132 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.314 Fit side-chains REVERT: A 104 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7573 (mtp) REVERT: B 369 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7172 (mtt-85) REVERT: C 40 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 369 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7042 (mtt-85) REVERT: D 371 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7434 (mmt) REVERT: D 378 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8670 (pm20) outliers start: 38 outliers final: 24 residues processed: 114 average time/residue: 0.4593 time to fit residues: 56.4022 Evaluate side-chains 122 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 92 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 195 THR 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 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 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 350 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 44 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 overall best weight: 0.9638 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.175734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130555 restraints weight = 6721.396| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.68 r_work: 0.3173 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- 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: 159 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 170 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1382 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= 0.138 Angle : 0.608 11.584 10874 Z= 0.307 Chirality : 0.043 0.134 1132 Planarity : 0.004 0.031 1416 Dihedral : 5.118 33.148 1101 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.22 % Allowed : 13.13 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.33 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.96 (0.25), residues: 446 loop : -0.39 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 369 TYR 0.011 0.002 TYR B 257 PHE 0.010 0.002 PHE D 177 TRP 0.011 0.002 TRP D 306 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7972) covalent geometry : angle 0.60423 (10854) SS BOND : bond 0.00339 ( 10) SS BOND : angle 1.76395 ( 20) hydrogen bonds : bond 0.03304 ( 285) hydrogen bonds : angle 4.95441 ( 762) *********************** 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 130 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.244 Fit side-chains REVERT: A 104 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7583 (mtp) REVERT: B 369 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7212 (mtt-85) REVERT: C 40 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7925 (mt) REVERT: C 66 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: D 369 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7077 (mtt-85) REVERT: D 371 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7370 (mmt) REVERT: D 378 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8669 (pm20) outliers start: 35 outliers final: 24 residues processed: 111 average time/residue: 0.4327 time to fit residues: 51.8086 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 : 0.341 ------------------------------------------------------------------------------- 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 92 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 195 THR 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 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 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 195 THR 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 Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 378 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.0000 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 overall best weight: 0.7686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.176427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131335 restraints weight = 6745.762| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.68 r_work: 0.3182 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 170 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 172 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1404 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= 0.123 Angle : 0.594 10.832 10874 Z= 0.300 Chirality : 0.042 0.136 1132 Planarity : 0.004 0.029 1416 Dihedral : 5.009 33.059 1101 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.98 % Allowed : 13.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.98 (0.25), residues: 446 loop : -0.36 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 67 TYR 0.014 0.002 TYR B 197 PHE 0.009 0.002 PHE B 281 TRP 0.010 0.001 TRP B 306 HIS 0.002 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7972) covalent geometry : angle 0.58835 (10854) SS BOND : bond 0.00320 ( 10) SS BOND : angle 2.02065 ( 20) hydrogen bonds : bond 0.03194 ( 285) hydrogen bonds : angle 4.84738 ( 762) *********************** 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 128 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.314 Fit side-chains REVERT: A 40 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7862 (mt) REVERT: A 104 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7591 (mtp) REVERT: B 369 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7203 (mtt-85) REVERT: C 40 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7934 (mt) REVERT: C 66 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 104 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7620 (mtp) REVERT: D 369 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7036 (mtt-85) REVERT: D 371 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7363 (mmt) REVERT: D 378 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8648 (pm20) outliers start: 33 outliers final: 21 residues processed: 111 average time/residue: 0.4933 time to fit residues: 58.8821 Evaluate side-chains 123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 92 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 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 104 MET 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 350 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.174715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129289 restraints weight = 6729.894| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.68 r_work: 0.3153 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 172 | |-----------------------------------------------------------------------------| |-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: 171 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7982 Z= 0.193 Angle : 0.667 10.713 10874 Z= 0.336 Chirality : 0.045 0.162 1132 Planarity : 0.005 0.033 1416 Dihedral : 5.325 33.429 1101 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.10 % Allowed : 13.73 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.25 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.87 (0.25), residues: 450 loop : -0.42 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 288 TYR 0.015 0.002 TYR D 257 PHE 0.013 0.002 PHE D 177 TRP 0.011 0.002 TRP B 306 HIS 0.004 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7972) covalent geometry : angle 0.65863 (10854) SS BOND : bond 0.00376 ( 10) SS BOND : angle 2.52612 ( 20) hydrogen bonds : bond 0.03588 ( 285) hydrogen bonds : angle 4.91365 ( 762) *********************** 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 126 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.324 Fit side-chains REVERT: A 104 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7606 (mtp) REVERT: B 369 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7207 (mtt-85) REVERT: C 40 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (mt) REVERT: C 66 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: C 104 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: D 369 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7046 (mtt-85) REVERT: D 371 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7438 (mmt) REVERT: D 378 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8661 (pm20) outliers start: 34 outliers final: 22 residues processed: 110 average time/residue: 0.4458 time to fit residues: 52.9562 Evaluate side-chains 121 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 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 195 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 96 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.177518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132441 restraints weight = 6724.890| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.68 r_work: 0.3194 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 171 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 178 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7982 Z= 0.105 Angle : 0.563 11.858 10874 Z= 0.284 Chirality : 0.041 0.126 1132 Planarity : 0.004 0.029 1416 Dihedral : 4.834 32.739 1101 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.61 % Allowed : 13.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.93 (0.25), residues: 452 loop : -0.27 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 88 TYR 0.012 0.001 TYR B 397 PHE 0.010 0.001 PHE B 281 TRP 0.009 0.001 TRP D 306 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7972) covalent geometry : angle 0.56034 (10854) SS BOND : bond 0.00275 ( 10) SS BOND : angle 1.46836 ( 20) hydrogen bonds : bond 0.02940 ( 285) hydrogen bonds : angle 4.71737 ( 762) ********************** 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 124 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.330 Fit side-chains REVERT: A 40 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 98 ASN cc_start: 0.6819 (m-40) cc_final: 0.6398 (m110) REVERT: A 104 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: B 369 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7227 (mtt-85) REVERT: C 40 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7958 (mt) REVERT: C 66 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: C 104 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7571 (mtp) REVERT: D 369 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7019 (mtt-85) REVERT: D 378 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8703 (pm20) outliers start: 30 outliers final: 15 residues processed: 111 average time/residue: 0.4802 time to fit residues: 57.3027 Evaluate side-chains 113 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain B residue 195 THR 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 100 VAL Chi-restraints excluded: chain C residue 104 MET 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 350 GLN Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain D residue 378 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 overall best weight: 1.0006 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.176280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130857 restraints weight = 6702.990| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.70 r_work: 0.3175 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 178 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 176 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1493 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= 0.139 Angle : 0.610 11.861 10874 Z= 0.306 Chirality : 0.043 0.146 1132 Planarity : 0.004 0.030 1416 Dihedral : 4.998 33.170 1101 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.53 % Allowed : 15.30 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: 0.40 (0.27), residues: 990 helix: None (None), residues: 0 sheet: 0.95 (0.25), residues: 450 loop : -0.31 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 67 TYR 0.012 0.002 TYR B 197 PHE 0.011 0.002 PHE D 177 TRP 0.010 0.002 TRP B 348 HIS 0.003 0.001 HIS D 405 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7972) covalent geometry : angle 0.60212 (10854) SS BOND : bond 0.00362 ( 10) SS BOND : angle 2.30140 ( 20) hydrogen bonds : bond 0.03215 ( 285) hydrogen bonds : angle 4.72886 ( 762) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.58 seconds wall clock time: 62 minutes 1.75 seconds (3721.75 seconds total)