Starting phenix.real_space_refine on Thu May 22 10:26:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.map" model { file = "/net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fml_50562/05_2025/9fml_50562.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 63 5.16 5 C 14707 2.51 5 N 4004 2.21 5 O 4487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23261 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "B" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "C" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "D" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "E" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "F" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Chain: "G" Number of atoms: 3323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3323 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 24, 'TRANS': 397} Time building chain proxies: 13.48, per 1000 atoms: 0.58 Number of scatterers: 23261 At special positions: 0 Unit cell: (174.84, 177.66, 114.68, 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 63 16.00 O 4487 8.00 N 4004 7.00 C 14707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " 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: 5.67 Conformation dependent library (CDL) restraints added in 3.0 seconds 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5334 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 21.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 181 through 184 removed outlier: 4.174A pdb=" N PHE A 184 " --> pdb=" O PRO A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 368 removed outlier: 6.629A pdb=" N GLY A 366 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 27 through 34 removed outlier: 3.515A pdb=" N VAL B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 112 through 123 Processing helix chain 'B' and resid 350 through 353 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 368 removed outlier: 6.630A pdb=" N GLY B 366 " --> pdb=" O TYR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 363 through 368 removed outlier: 6.564A pdb=" N GLY C 366 " --> pdb=" O TYR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 59 through 62 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 181 through 184 removed outlier: 4.195A pdb=" N PHE D 184 " --> pdb=" O PRO D 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 363 through 368 removed outlier: 6.626A pdb=" N GLY D 366 " --> pdb=" O TYR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 112 through 123 Processing helix chain 'E' and resid 181 through 184 removed outlier: 4.039A pdb=" N PHE E 184 " --> pdb=" O PRO E 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'E' and resid 363 through 368 removed outlier: 6.609A pdb=" N GLY E 366 " --> pdb=" O TYR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 59 through 62 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 350 through 353 Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'F' and resid 363 through 368 removed outlier: 6.589A pdb=" N GLY F 366 " --> pdb=" O TYR F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.529A pdb=" N THR F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 59 through 62 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 112 through 123 Processing helix chain 'G' and resid 181 through 184 removed outlier: 4.079A pdb=" N PHE G 184 " --> pdb=" O PRO G 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 350 through 353 Processing helix chain 'G' and resid 354 through 362 Processing helix chain 'G' and resid 363 through 368 removed outlier: 6.625A pdb=" N GLY G 366 " --> pdb=" O TYR G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 96 current: chain 'A' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 179 current: chain 'A' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 345 current: chain 'B' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 179 current: chain 'B' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 345 current: chain 'C' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 179 current: chain 'C' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 345 current: chain 'D' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 179 current: chain 'D' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 345 current: chain 'E' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 179 current: chain 'E' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 338 through 345 current: chain 'F' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 289 through 321 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 345 current: chain 'G' and resid 148 through 153 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 179 current: chain 'G' and resid 289 through 321 Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 247 removed outlier: 6.453A pdb=" N GLU A 252 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS B 244 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU B 252 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS C 244 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 252 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS D 244 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU D 252 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS E 244 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU E 252 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS F 244 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU F 252 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS G 244 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU G 252 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 244 " --> pdb=" O GLU G 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 10 through 12 current: chain 'B' and resid 54 through 57 Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 54 through 57 880 hydrogen bonds defined for protein. 2481 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: 6.47 Time building geometry restraints manager: 6.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7623 1.34 - 1.46: 5737 1.46 - 1.58: 10475 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 23933 Sorted by residual: bond pdb=" CG LEU A 277 " pdb=" CD1 LEU A 277 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CG LEU E 277 " pdb=" CD1 LEU E 277 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.10e+00 bond pdb=" CA HIS G 332 " pdb=" CB HIS G 332 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.43e+00 bond pdb=" CG LEU D 277 " pdb=" CD1 LEU D 277 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CG LEU C 277 " pdb=" CD1 LEU C 277 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.68e-01 ... (remaining 23928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 32150 1.82 - 3.65: 499 3.65 - 5.47: 19 5.47 - 7.30: 0 7.30 - 9.12: 8 Bond angle restraints: 32676 Sorted by residual: angle pdb=" CB MET E 57 " pdb=" CG MET E 57 " pdb=" SD MET E 57 " ideal model delta sigma weight residual 112.70 121.28 -8.58 3.00e+00 1.11e-01 8.19e+00 angle pdb=" CA LEU F 277 " pdb=" CB LEU F 277 " pdb=" CG LEU F 277 " ideal model delta sigma weight residual 116.30 107.18 9.12 3.50e+00 8.16e-02 6.79e+00 angle pdb=" CA LEU A 277 " pdb=" CB LEU A 277 " pdb=" CG LEU A 277 " ideal model delta sigma weight residual 116.30 107.20 9.10 3.50e+00 8.16e-02 6.76e+00 angle pdb=" CA LEU C 277 " pdb=" CB LEU C 277 " pdb=" CG LEU C 277 " ideal model delta sigma weight residual 116.30 107.21 9.09 3.50e+00 8.16e-02 6.75e+00 angle pdb=" CA LEU E 277 " pdb=" CB LEU E 277 " pdb=" CG LEU E 277 " ideal model delta sigma weight residual 116.30 107.53 8.77 3.50e+00 8.16e-02 6.27e+00 ... (remaining 32671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12771 17.92 - 35.83: 831 35.83 - 53.75: 202 53.75 - 71.66: 52 71.66 - 89.58: 32 Dihedral angle restraints: 13888 sinusoidal: 5460 harmonic: 8428 Sorted by residual: dihedral pdb=" CA ALA G 310 " pdb=" C ALA G 310 " pdb=" N ASP G 311 " pdb=" CA ASP G 311 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA E 310 " pdb=" C ALA E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA C 310 " pdb=" C ALA C 310 " pdb=" N ASP C 311 " pdb=" CA ASP C 311 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 13885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1846 0.030 - 0.059: 985 0.059 - 0.089: 275 0.089 - 0.119: 227 0.119 - 0.148: 76 Chirality restraints: 3409 Sorted by residual: chirality pdb=" CB VAL E 281 " pdb=" CA VAL E 281 " pdb=" CG1 VAL E 281 " pdb=" CG2 VAL E 281 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE F 416 " pdb=" N ILE F 416 " pdb=" C ILE F 416 " pdb=" CB ILE F 416 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CB VAL C 281 " pdb=" CA VAL C 281 " pdb=" CG1 VAL C 281 " pdb=" CG2 VAL C 281 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 3406 not shown) Planarity restraints: 4263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP G 370 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C TRP G 370 " 0.032 2.00e-02 2.50e+03 pdb=" O TRP G 370 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP G 371 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 370 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C TRP D 370 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP D 370 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP D 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP F 370 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.98e+00 pdb=" C TRP F 370 " 0.030 2.00e-02 2.50e+03 pdb=" O TRP F 370 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP F 371 " -0.010 2.00e-02 2.50e+03 ... (remaining 4260 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4681 2.79 - 3.32: 20554 3.32 - 3.85: 41038 3.85 - 4.37: 47168 4.37 - 4.90: 80910 Nonbonded interactions: 194351 Sorted by model distance: nonbonded pdb=" OH TYR D 357 " pdb=" OE1 GLU D 367 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP F 222 " pdb=" OG SER F 276 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP D 222 " pdb=" OG SER D 276 " model vdw 2.293 3.040 nonbonded pdb=" OD1 ASP E 222 " pdb=" OG SER E 276 " model vdw 2.302 3.040 nonbonded pdb=" NZ LYS D 35 " pdb=" O GLY D 63 " model vdw 2.345 3.120 ... (remaining 194346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 48.760 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 0.048 23947 Z= 0.149 Angle : 0.590 9.123 32704 Z= 0.332 Chirality : 0.047 0.148 3409 Planarity : 0.004 0.040 4263 Dihedral : 13.874 89.577 8512 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.57 % Allowed : 8.87 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 2940 helix: 0.80 (0.23), residues: 497 sheet: 1.54 (0.14), residues: 1029 loop : -0.19 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 370 HIS 0.005 0.001 HIS G 341 PHE 0.022 0.003 PHE E 321 TYR 0.014 0.002 TYR C 304 ARG 0.004 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.13532 ( 880) hydrogen bonds : angle 6.14141 ( 2481) SS BOND : bond 0.00197 ( 14) SS BOND : angle 0.90652 ( 28) covalent geometry : bond 0.00292 (23933) covalent geometry : angle 0.58954 (32676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 2.363 Fit side-chains REVERT: A 29 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6370 (tp30) REVERT: A 385 MET cc_start: 0.8985 (mmm) cc_final: 0.8631 (mmm) REVERT: B 8 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: B 258 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 277 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8222 (tt) REVERT: C 72 ASN cc_start: 0.6825 (OUTLIER) cc_final: 0.6137 (p0) REVERT: D 2 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: D 57 MET cc_start: 0.7143 (mtp) cc_final: 0.6886 (mtp) REVERT: D 185 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8267 (mtpt) REVERT: E 8 GLN cc_start: 0.7723 (mt0) cc_final: 0.7384 (mt0) REVERT: F 2 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: F 42 MET cc_start: 0.6435 (mtp) cc_final: 0.5801 (mtp) REVERT: F 258 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: F 277 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8570 (tt) REVERT: G 57 MET cc_start: 0.7089 (mtp) cc_final: 0.6559 (mtp) REVERT: G 277 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8413 (tp) outliers start: 39 outliers final: 24 residues processed: 270 average time/residue: 1.5360 time to fit residues: 465.8650 Evaluate side-chains 269 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 383 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 195 GLN B 335 ASN C 174 ASN C 178 ASN E 178 ASN F 195 GLN G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135508 restraints weight = 17684.495| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.74 r_work: 0.3159 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work: 0.2879 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23947 Z= 0.183 Angle : 0.625 11.912 32704 Z= 0.340 Chirality : 0.049 0.215 3409 Planarity : 0.005 0.036 4263 Dihedral : 7.561 84.035 3292 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.85 % Allowed : 8.91 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.14), residues: 2940 helix: 0.97 (0.22), residues: 504 sheet: 1.41 (0.14), residues: 1029 loop : -0.23 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 373 HIS 0.006 0.002 HIS E 341 PHE 0.025 0.003 PHE E 321 TYR 0.014 0.002 TYR C 357 ARG 0.005 0.001 ARG F 356 Details of bonding type rmsd hydrogen bonds : bond 0.05429 ( 880) hydrogen bonds : angle 5.40331 ( 2481) SS BOND : bond 0.00279 ( 14) SS BOND : angle 0.94984 ( 28) covalent geometry : bond 0.00386 (23933) covalent geometry : angle 0.62468 (32676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 2.513 Fit side-chains REVERT: A 29 GLU cc_start: 0.6382 (mm-30) cc_final: 0.5878 (tp30) REVERT: A 385 MET cc_start: 0.9003 (mmm) cc_final: 0.8708 (mmm) REVERT: B 277 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8382 (tt) REVERT: B 378 GLN cc_start: 0.8134 (tt0) cc_final: 0.7799 (tm-30) REVERT: D 2 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: D 57 MET cc_start: 0.7001 (mtp) cc_final: 0.6673 (mtp) REVERT: E 8 GLN cc_start: 0.7669 (mt0) cc_final: 0.7351 (mt0) REVERT: E 171 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8659 (mptt) REVERT: F 2 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: F 29 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5855 (tm-30) REVERT: F 277 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8629 (tt) REVERT: G 29 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6000 (tm-30) REVERT: G 277 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 46 outliers final: 21 residues processed: 273 average time/residue: 1.5068 time to fit residues: 463.3824 Evaluate side-chains 266 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 87 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN F 195 GLN G 8 GLN G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138257 restraints weight = 17834.882| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.76 r_work: 0.3146 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work: 0.2872 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23947 Z= 0.201 Angle : 0.648 12.256 32704 Z= 0.354 Chirality : 0.050 0.236 3409 Planarity : 0.005 0.037 4263 Dihedral : 7.277 83.101 3265 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.25 % Allowed : 9.55 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 2940 helix: 0.98 (0.22), residues: 504 sheet: 1.32 (0.14), residues: 994 loop : -0.21 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 373 HIS 0.007 0.002 HIS E 341 PHE 0.026 0.003 PHE E 321 TYR 0.015 0.003 TYR E 233 ARG 0.005 0.001 ARG F 356 Details of bonding type rmsd hydrogen bonds : bond 0.05651 ( 880) hydrogen bonds : angle 5.44911 ( 2481) SS BOND : bond 0.00314 ( 14) SS BOND : angle 1.04564 ( 28) covalent geometry : bond 0.00427 (23933) covalent geometry : angle 0.64798 (32676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 2.692 Fit side-chains REVERT: A 385 MET cc_start: 0.9022 (mmm) cc_final: 0.8688 (mmm) REVERT: B 8 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: B 277 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8441 (tt) REVERT: B 378 GLN cc_start: 0.8118 (tt0) cc_final: 0.7785 (tm-30) REVERT: C 8 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: D 2 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: D 57 MET cc_start: 0.7008 (mtp) cc_final: 0.6718 (mtp) REVERT: E 8 GLN cc_start: 0.7727 (mt0) cc_final: 0.7434 (mt0) REVERT: E 171 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8636 (mptt) REVERT: F 2 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: F 29 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5835 (tm-30) REVERT: F 277 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8600 (tt) REVERT: G 29 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5936 (tm-30) REVERT: G 140 MET cc_start: 0.8602 (mmm) cc_final: 0.8366 (mmm) REVERT: G 277 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8476 (tt) REVERT: G 350 ASP cc_start: 0.9082 (p0) cc_final: 0.8876 (p0) outliers start: 56 outliers final: 31 residues processed: 281 average time/residue: 1.5383 time to fit residues: 486.6097 Evaluate side-chains 278 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 225 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 228 optimal weight: 0.4980 chunk 248 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 111 ASN C 174 ASN C 178 ASN F 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.170635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145558 restraints weight = 18151.388| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.72 r_work: 0.3197 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work: 0.2934 rms_B_bonded: 4.21 restraints_weight: 0.1250 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23947 Z= 0.116 Angle : 0.528 9.227 32704 Z= 0.286 Chirality : 0.046 0.139 3409 Planarity : 0.003 0.034 4263 Dihedral : 6.890 81.026 3265 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.73 % Allowed : 10.75 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 2940 helix: 1.25 (0.23), residues: 504 sheet: 1.34 (0.14), residues: 1036 loop : -0.16 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 373 HIS 0.003 0.001 HIS G 341 PHE 0.020 0.002 PHE E 321 TYR 0.011 0.002 TYR E 357 ARG 0.004 0.000 ARG E 288 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 880) hydrogen bonds : angle 5.15357 ( 2481) SS BOND : bond 0.00175 ( 14) SS BOND : angle 0.70391 ( 28) covalent geometry : bond 0.00239 (23933) covalent geometry : angle 0.52821 (32676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 2.691 Fit side-chains REVERT: A 29 GLU cc_start: 0.6316 (mm-30) cc_final: 0.5849 (tp30) REVERT: A 385 MET cc_start: 0.8949 (mmm) cc_final: 0.8744 (mmm) REVERT: B 378 GLN cc_start: 0.8021 (tt0) cc_final: 0.7705 (tm-30) REVERT: C 8 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7349 (mt0) REVERT: D 57 MET cc_start: 0.6945 (mtp) cc_final: 0.6645 (mtp) REVERT: E 8 GLN cc_start: 0.7640 (mt0) cc_final: 0.7345 (mt0) REVERT: E 171 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8521 (mptt) REVERT: F 29 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5898 (tm-30) REVERT: G 29 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5936 (tm-30) outliers start: 43 outliers final: 23 residues processed: 268 average time/residue: 1.4875 time to fit residues: 450.3564 Evaluate side-chains 257 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 250 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN D 243 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 195 GLN G 8 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.164045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137952 restraints weight = 18013.539| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 0.74 r_work: 0.3169 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work: 0.2885 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23947 Z= 0.215 Angle : 0.656 12.443 32704 Z= 0.358 Chirality : 0.050 0.197 3409 Planarity : 0.005 0.035 4263 Dihedral : 6.804 80.568 3253 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.05 % Allowed : 10.43 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 2940 helix: 1.06 (0.23), residues: 504 sheet: 1.32 (0.14), residues: 994 loop : -0.21 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 373 HIS 0.007 0.002 HIS E 341 PHE 0.028 0.003 PHE E 321 TYR 0.016 0.003 TYR C 357 ARG 0.006 0.001 ARG C 391 Details of bonding type rmsd hydrogen bonds : bond 0.05651 ( 880) hydrogen bonds : angle 5.42216 ( 2481) SS BOND : bond 0.00339 ( 14) SS BOND : angle 1.05858 ( 28) covalent geometry : bond 0.00458 (23933) covalent geometry : angle 0.65542 (32676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 2.438 Fit side-chains REVERT: A 385 MET cc_start: 0.9012 (mmm) cc_final: 0.8679 (mmm) REVERT: B 8 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: B 277 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 378 GLN cc_start: 0.8101 (tt0) cc_final: 0.7777 (tm-30) REVERT: C 8 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: D 57 MET cc_start: 0.7005 (mtp) cc_final: 0.6668 (mtp) REVERT: E 8 GLN cc_start: 0.7687 (mt0) cc_final: 0.7456 (mt0) REVERT: E 171 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8642 (mptt) REVERT: F 2 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: F 29 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5838 (tm-30) REVERT: F 277 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8625 (tt) REVERT: G 8 GLN cc_start: 0.7556 (mt0) cc_final: 0.7350 (mt0) REVERT: G 29 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6019 (tm-30) REVERT: G 258 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: G 277 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8432 (tt) outliers start: 51 outliers final: 29 residues processed: 276 average time/residue: 1.4955 time to fit residues: 465.8919 Evaluate side-chains 271 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 108 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 270 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 163 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN D 263 GLN E 72 ASN F 195 GLN G 174 ASN G 178 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.163558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137433 restraints weight = 17917.706| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.73 r_work: 0.3156 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work: 0.2878 rms_B_bonded: 4.36 restraints_weight: 0.1250 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23947 Z= 0.255 Angle : 0.706 13.068 32704 Z= 0.388 Chirality : 0.052 0.225 3409 Planarity : 0.005 0.038 4263 Dihedral : 6.936 81.467 3253 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.29 % Allowed : 10.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 2940 helix: 0.91 (0.22), residues: 504 sheet: 1.28 (0.14), residues: 994 loop : -0.28 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 373 HIS 0.009 0.002 HIS E 341 PHE 0.029 0.004 PHE E 321 TYR 0.019 0.003 TYR G 233 ARG 0.007 0.001 ARG C 391 Details of bonding type rmsd hydrogen bonds : bond 0.06052 ( 880) hydrogen bonds : angle 5.52944 ( 2481) SS BOND : bond 0.00400 ( 14) SS BOND : angle 1.21988 ( 28) covalent geometry : bond 0.00550 (23933) covalent geometry : angle 0.70496 (32676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 2.568 Fit side-chains REVERT: A 385 MET cc_start: 0.9038 (mmm) cc_final: 0.8695 (mmm) REVERT: B 8 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: B 57 MET cc_start: 0.7030 (mtp) cc_final: 0.6639 (mtm) REVERT: B 277 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8380 (tt) REVERT: B 378 GLN cc_start: 0.8045 (tt0) cc_final: 0.7722 (tm-30) REVERT: C 8 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: D 2 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: D 57 MET cc_start: 0.7032 (mtp) cc_final: 0.6736 (mtp) REVERT: E 171 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8585 (mptt) REVERT: F 2 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: F 29 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5779 (tm-30) REVERT: F 277 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8697 (tt) REVERT: G 8 GLN cc_start: 0.7573 (mt0) cc_final: 0.7323 (mt0) REVERT: G 29 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5946 (tm-30) REVERT: G 258 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: G 277 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8501 (tp) outliers start: 57 outliers final: 32 residues processed: 275 average time/residue: 1.6181 time to fit residues: 499.9962 Evaluate side-chains 271 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.165707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138112 restraints weight = 18028.888| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.74 r_work: 0.3159 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.2898 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23947 Z= 0.168 Angle : 0.602 11.233 32704 Z= 0.328 Chirality : 0.048 0.162 3409 Planarity : 0.004 0.037 4263 Dihedral : 6.718 79.694 3253 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.97 % Allowed : 10.75 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 2940 helix: 1.08 (0.23), residues: 504 sheet: 1.33 (0.14), residues: 994 loop : -0.23 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 373 HIS 0.005 0.001 HIS E 341 PHE 0.024 0.003 PHE E 321 TYR 0.014 0.002 TYR C 357 ARG 0.004 0.001 ARG E 288 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 880) hydrogen bonds : angle 5.33589 ( 2481) SS BOND : bond 0.00272 ( 14) SS BOND : angle 0.95177 ( 28) covalent geometry : bond 0.00356 (23933) covalent geometry : angle 0.60181 (32676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 2.636 Fit side-chains REVERT: A 29 GLU cc_start: 0.6394 (mm-30) cc_final: 0.5915 (tp30) REVERT: A 385 MET cc_start: 0.8988 (mmm) cc_final: 0.8681 (mmm) REVERT: B 8 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: B 277 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8302 (tt) REVERT: B 378 GLN cc_start: 0.8094 (tt0) cc_final: 0.7785 (tm-30) REVERT: C 8 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7388 (mt0) REVERT: D 2 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: D 57 MET cc_start: 0.7047 (mtp) cc_final: 0.6723 (mtp) REVERT: E 171 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8606 (mptt) REVERT: F 2 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7139 (mm-30) REVERT: F 7 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6899 (p0) REVERT: F 29 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5854 (tm-30) REVERT: F 277 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8578 (tt) REVERT: G 8 GLN cc_start: 0.7570 (mt0) cc_final: 0.7325 (mt0) REVERT: G 29 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6011 (tm-30) REVERT: G 258 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: G 277 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8432 (tt) outliers start: 49 outliers final: 32 residues processed: 275 average time/residue: 1.5461 time to fit residues: 480.2057 Evaluate side-chains 275 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 280 optimal weight: 0.1980 chunk 111 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 134 optimal weight: 0.0770 chunk 233 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN E 72 ASN F 195 GLN G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.165078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.139440 restraints weight = 17891.733| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 0.71 r_work: 0.3178 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work: 0.2903 rms_B_bonded: 4.20 restraints_weight: 0.1250 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23947 Z= 0.171 Angle : 0.605 10.982 32704 Z= 0.329 Chirality : 0.048 0.164 3409 Planarity : 0.004 0.037 4263 Dihedral : 6.707 79.537 3253 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.21 % Allowed : 10.63 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 2940 helix: 1.08 (0.23), residues: 504 sheet: 1.33 (0.14), residues: 994 loop : -0.22 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 373 HIS 0.006 0.002 HIS E 341 PHE 0.025 0.003 PHE E 321 TYR 0.014 0.002 TYR C 357 ARG 0.004 0.001 ARG C 391 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 880) hydrogen bonds : angle 5.33022 ( 2481) SS BOND : bond 0.00263 ( 14) SS BOND : angle 0.93917 ( 28) covalent geometry : bond 0.00362 (23933) covalent geometry : angle 0.60444 (32676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 2.460 Fit side-chains REVERT: A 29 GLU cc_start: 0.6322 (mm-30) cc_final: 0.5831 (tp30) REVERT: A 385 MET cc_start: 0.9003 (mmm) cc_final: 0.8680 (mmm) REVERT: B 8 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: B 57 MET cc_start: 0.6910 (mtp) cc_final: 0.6427 (mtm) REVERT: B 277 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8311 (tt) REVERT: B 378 GLN cc_start: 0.8052 (tt0) cc_final: 0.7730 (tm-30) REVERT: C 8 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: D 2 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: D 57 MET cc_start: 0.6999 (mtp) cc_final: 0.6671 (mtp) REVERT: E 57 MET cc_start: 0.6970 (mtm) cc_final: 0.6737 (mtp) REVERT: E 171 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8581 (mptt) REVERT: F 2 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: F 29 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: F 277 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8588 (tt) REVERT: G 8 GLN cc_start: 0.7555 (mt0) cc_final: 0.7302 (mt0) REVERT: G 29 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: G 258 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: G 277 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8428 (tt) outliers start: 55 outliers final: 33 residues processed: 272 average time/residue: 1.4755 time to fit residues: 451.8404 Evaluate side-chains 276 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 253 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN D 8 GLN D 72 ASN D 111 ASN E 72 ASN E 111 ASN F 72 ASN F 195 GLN G 111 ASN G 132 HIS G 178 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137577 restraints weight = 17987.634| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.73 r_work: 0.3205 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23947 Z= 0.097 Angle : 0.498 8.382 32704 Z= 0.268 Chirality : 0.045 0.138 3409 Planarity : 0.003 0.036 4263 Dihedral : 6.187 72.332 3253 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.77 % Allowed : 11.16 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 2940 helix: 1.38 (0.23), residues: 504 sheet: 1.34 (0.14), residues: 1036 loop : -0.13 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 373 HIS 0.003 0.001 HIS C 341 PHE 0.017 0.001 PHE E 321 TYR 0.010 0.001 TYR D 330 ARG 0.004 0.000 ARG G 10 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 880) hydrogen bonds : angle 5.02312 ( 2481) SS BOND : bond 0.00121 ( 14) SS BOND : angle 0.67272 ( 28) covalent geometry : bond 0.00199 (23933) covalent geometry : angle 0.49738 (32676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 2.394 Fit side-chains REVERT: A 29 GLU cc_start: 0.6396 (mm-30) cc_final: 0.5909 (tp30) REVERT: A 242 LYS cc_start: 0.8356 (ttmm) cc_final: 0.7839 (tttt) REVERT: B 57 MET cc_start: 0.7023 (mtp) cc_final: 0.6659 (mtm) REVERT: B 288 ARG cc_start: 0.8783 (mmt180) cc_final: 0.8558 (mmt180) REVERT: B 378 GLN cc_start: 0.8099 (tt0) cc_final: 0.7795 (tm-30) REVERT: C 350 ASP cc_start: 0.8833 (p0) cc_final: 0.8623 (p0) REVERT: D 2 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: D 57 MET cc_start: 0.7080 (mtp) cc_final: 0.6761 (mtp) REVERT: E 171 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8525 (mptt) REVERT: F 2 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: F 29 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6280 (mm-30) REVERT: F 258 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: F 277 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8442 (tt) REVERT: G 29 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6166 (tm-30) REVERT: G 350 ASP cc_start: 0.8948 (p0) cc_final: 0.8701 (p0) outliers start: 44 outliers final: 26 residues processed: 282 average time/residue: 1.4598 time to fit residues: 466.7648 Evaluate side-chains 271 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 279 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 271 optimal weight: 0.0060 chunk 197 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 54 optimal weight: 0.0570 chunk 258 optimal weight: 9.9990 overall best weight: 2.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN E 72 ASN F 195 GLN G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.165965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.138089 restraints weight = 17841.372| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 0.75 r_work: 0.3220 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23947 Z= 0.135 Angle : 0.553 9.610 32704 Z= 0.298 Chirality : 0.047 0.139 3409 Planarity : 0.004 0.036 4263 Dihedral : 6.278 72.599 3248 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 11.56 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 2940 helix: 1.30 (0.23), residues: 504 sheet: 1.34 (0.14), residues: 1036 loop : -0.14 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 373 HIS 0.005 0.001 HIS E 341 PHE 0.022 0.002 PHE E 321 TYR 0.013 0.002 TYR E 357 ARG 0.003 0.000 ARG G 10 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 880) hydrogen bonds : angle 5.16579 ( 2481) SS BOND : bond 0.00212 ( 14) SS BOND : angle 0.79444 ( 28) covalent geometry : bond 0.00285 (23933) covalent geometry : angle 0.55235 (32676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5880 Ramachandran restraints generated. 2940 Oldfield, 0 Emsley, 2940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 2.393 Fit side-chains REVERT: B 288 ARG cc_start: 0.8816 (mmt180) cc_final: 0.8595 (mmt180) REVERT: B 378 GLN cc_start: 0.8112 (tt0) cc_final: 0.7830 (tm-30) REVERT: D 2 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: D 8 GLN cc_start: 0.7649 (mt0) cc_final: 0.7444 (mm-40) REVERT: D 57 MET cc_start: 0.7166 (mtp) cc_final: 0.6859 (mtp) REVERT: E 171 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (mptt) REVERT: F 2 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: F 7 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6895 (p0) REVERT: F 29 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6316 (mm-30) REVERT: F 258 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: F 277 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8498 (tt) REVERT: G 29 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6121 (tm-30) REVERT: G 277 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8310 (tt) outliers start: 36 outliers final: 24 residues processed: 263 average time/residue: 1.5115 time to fit residues: 452.0769 Evaluate side-chains 263 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 2 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain F residue 2 GLU Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 69 optimal weight: 6.9990 chunk 135 optimal weight: 0.0070 chunk 76 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 223 optimal weight: 0.0070 chunk 195 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 195 GLN B 195 GLN C 174 ASN C 178 ASN D 72 ASN F 195 GLN G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.167928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140341 restraints weight = 17941.377| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.77 r_work: 0.3263 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23947 Z= 0.092 Angle : 0.484 7.675 32704 Z= 0.259 Chirality : 0.045 0.138 3409 Planarity : 0.003 0.036 4263 Dihedral : 5.895 66.981 3248 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.24 % Allowed : 11.92 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 2940 helix: 1.50 (0.23), residues: 504 sheet: 1.44 (0.14), residues: 1043 loop : -0.01 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 373 HIS 0.003 0.001 HIS B 341 PHE 0.015 0.001 PHE E 321 TYR 0.010 0.001 TYR E 363 ARG 0.003 0.000 ARG G 10 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 880) hydrogen bonds : angle 4.94025 ( 2481) SS BOND : bond 0.00110 ( 14) SS BOND : angle 0.62623 ( 28) covalent geometry : bond 0.00190 (23933) covalent geometry : angle 0.48423 (32676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24371.19 seconds wall clock time: 419 minutes 16.07 seconds (25156.07 seconds total)