Starting phenix.real_space_refine on Fri Sep 19 03:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fml_50562/09_2025/9fml_50562.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fml_50562/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fml_50562/09_2025/9fml_50562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fml_50562/09_2025/9fml_50562.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fml_50562/09_2025/9fml_50562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fml_50562/09_2025/9fml_50562.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.85, per 1000 atoms: 0.25 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: 1.83 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.73 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: 3.91 Time building geometry restraints manager: 2.55 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: 0.01 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.770 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (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 ARG 0.004 0.001 ARG A 194 TYR 0.014 0.002 TYR C 304 PHE 0.022 0.003 PHE E 321 TRP 0.015 0.002 TRP G 370 HIS 0.005 0.001 HIS G 341 Details of bonding type rmsd covalent geometry : bond 0.00292 (23933) covalent geometry : angle 0.58954 (32676) SS BOND : bond 0.00197 ( 14) SS BOND : angle 0.90652 ( 28) hydrogen bonds : bond 0.13532 ( 880) hydrogen bonds : angle 6.14141 ( 2481) *********************** 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 : 0.896 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: 0.7820 time to fit residues: 236.1995 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 : 0.859 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.164062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.135072 restraints weight = 17757.892| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.78 r_work: 0.3176 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23947 Z= 0.221 Angle : 0.674 12.718 32704 Z= 0.368 Chirality : 0.051 0.253 3409 Planarity : 0.005 0.038 4263 Dihedral : 7.700 83.858 3292 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 8.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 2940 helix: 0.86 (0.22), residues: 504 sheet: 1.37 (0.14), residues: 1029 loop : -0.28 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 356 TYR 0.016 0.003 TYR C 357 PHE 0.027 0.004 PHE E 321 TRP 0.021 0.002 TRP E 373 HIS 0.008 0.002 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00474 (23933) covalent geometry : angle 0.67350 (32676) SS BOND : bond 0.00316 ( 14) SS BOND : angle 1.09796 ( 28) hydrogen bonds : bond 0.05971 ( 880) hydrogen bonds : angle 5.51022 ( 2481) *********************** 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 280 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.927 Fit side-chains REVERT: A 29 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6020 (tp30) REVERT: A 385 MET cc_start: 0.9037 (mmm) cc_final: 0.8733 (mmm) REVERT: B 277 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8371 (tt) REVERT: B 378 GLN cc_start: 0.8030 (tt0) cc_final: 0.7748 (tm-30) REVERT: D 2 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7295 (mm-30) REVERT: D 57 MET cc_start: 0.7119 (mtp) cc_final: 0.6834 (mtp) REVERT: E 8 GLN cc_start: 0.7802 (mt0) cc_final: 0.7503 (mt0) REVERT: E 171 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8525 (mptt) REVERT: F 2 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: F 29 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: F 277 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8587 (tt) REVERT: G 29 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: G 277 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8437 (tt) REVERT: G 350 ASP cc_start: 0.8990 (p0) cc_final: 0.8766 (p0) outliers start: 50 outliers final: 24 residues processed: 270 average time/residue: 0.7416 time to fit residues: 224.9336 Evaluate side-chains 261 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 264 SER 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 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 171 LYS 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 276 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.163776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135196 restraints weight = 17756.221| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.75 r_work: 0.3149 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work: 0.2880 rms_B_bonded: 4.81 restraints_weight: 0.1250 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23947 Z= 0.160 Angle : 0.589 11.030 32704 Z= 0.320 Chirality : 0.048 0.193 3409 Planarity : 0.004 0.035 4263 Dihedral : 7.162 82.741 3270 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.01 % Allowed : 9.87 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.14), residues: 2940 helix: 1.08 (0.23), residues: 504 sheet: 1.34 (0.14), residues: 1029 loop : -0.25 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 288 TYR 0.013 0.002 TYR E 357 PHE 0.023 0.003 PHE E 321 TRP 0.016 0.002 TRP G 373 HIS 0.005 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00337 (23933) covalent geometry : angle 0.58866 (32676) SS BOND : bond 0.00249 ( 14) SS BOND : angle 0.88719 ( 28) hydrogen bonds : bond 0.04980 ( 880) hydrogen bonds : angle 5.32843 ( 2481) *********************** 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 288 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 0.667 Fit side-chains REVERT: A 385 MET cc_start: 0.8987 (mmm) cc_final: 0.8761 (mmm) REVERT: B 8 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: B 277 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 378 GLN cc_start: 0.8120 (tt0) cc_final: 0.7788 (tm-30) REVERT: C 8 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7507 (mt0) REVERT: D 2 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: D 57 MET cc_start: 0.6998 (mtp) cc_final: 0.6697 (mtp) REVERT: E 8 GLN cc_start: 0.7724 (mt0) cc_final: 0.7426 (mt0) REVERT: E 171 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8638 (mptt) REVERT: F 2 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: F 29 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: F 277 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8545 (tt) REVERT: G 29 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6024 (tm-30) REVERT: G 277 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8530 (tt) outliers start: 50 outliers final: 25 residues processed: 276 average time/residue: 0.7719 time to fit residues: 239.8743 Evaluate side-chains 268 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 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 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 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 188 optimal weight: 0.5980 chunk 127 optimal weight: 0.0070 chunk 191 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.138875 restraints weight = 18080.614| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 0.71 r_work: 0.3220 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work: 0.2942 rms_B_bonded: 4.91 restraints_weight: 0.1250 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23947 Z= 0.102 Angle : 0.502 8.566 32704 Z= 0.271 Chirality : 0.045 0.139 3409 Planarity : 0.003 0.033 4263 Dihedral : 6.730 80.158 3265 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.48 % Allowed : 10.75 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.14), residues: 2940 helix: 1.36 (0.23), residues: 504 sheet: 1.36 (0.14), residues: 1036 loop : -0.09 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 288 TYR 0.010 0.001 TYR C 304 PHE 0.018 0.002 PHE E 321 TRP 0.013 0.001 TRP B 373 HIS 0.004 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00209 (23933) covalent geometry : angle 0.50163 (32676) SS BOND : bond 0.00144 ( 14) SS BOND : angle 0.62119 ( 28) hydrogen bonds : bond 0.03757 ( 880) hydrogen bonds : angle 5.04895 ( 2481) *********************** 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: 37 poor density : 243 time to evaluate : 0.889 Fit side-chains REVERT: A 29 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6063 (tp30) REVERT: B 8 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: B 378 GLN cc_start: 0.8098 (tt0) cc_final: 0.7803 (tm-30) REVERT: D 57 MET cc_start: 0.7026 (mtp) cc_final: 0.6737 (mtp) REVERT: E 8 GLN cc_start: 0.7689 (mt0) cc_final: 0.7438 (mt0) REVERT: E 171 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8578 (mptt) REVERT: F 29 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.6350 (mm-30) REVERT: F 258 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: G 29 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: G 258 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7598 (tt0) outliers start: 37 outliers final: 19 residues processed: 271 average time/residue: 0.7094 time to fit residues: 216.7424 Evaluate side-chains 260 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 8 GLN Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain C residue 55 VAL 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 D residue 408 SER 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 249 LEU Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain G residue 29 GLU Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 258 GLU 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 75 optimal weight: 0.0170 chunk 261 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.5424 ------------------------------------------------------------------------------- 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 8 GLN F 195 GLN G 8 GLN G 178 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.164414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136181 restraints weight = 17728.101| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.74 r_work: 0.3172 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23947 Z= 0.138 Angle : 0.553 10.072 32704 Z= 0.298 Chirality : 0.047 0.140 3409 Planarity : 0.004 0.033 4263 Dihedral : 6.361 79.549 3248 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 10.79 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.14), residues: 2940 helix: 1.29 (0.23), residues: 504 sheet: 1.34 (0.14), residues: 1036 loop : -0.11 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 391 TYR 0.011 0.002 TYR G 304 PHE 0.022 0.002 PHE E 321 TRP 0.014 0.002 TRP G 373 HIS 0.005 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00288 (23933) covalent geometry : angle 0.55247 (32676) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.77846 ( 28) hydrogen bonds : bond 0.04481 ( 880) hydrogen bonds : angle 5.16669 ( 2481) *********************** 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 284 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.980 Fit side-chains REVERT: A 385 MET cc_start: 0.9044 (mmm) cc_final: 0.8789 (mmm) REVERT: B 8 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: B 277 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8217 (tt) REVERT: B 378 GLN cc_start: 0.8016 (tt0) cc_final: 0.7750 (tm-30) REVERT: C 8 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: D 57 MET cc_start: 0.7131 (mtp) cc_final: 0.6886 (mtp) REVERT: E 2 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: E 8 GLN cc_start: 0.7705 (mt0) cc_final: 0.7459 (mt0) REVERT: E 171 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8446 (mptt) REVERT: F 2 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: F 29 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6018 (tm-30) REVERT: F 258 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: F 277 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8485 (tt) REVERT: G 29 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: G 258 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: G 277 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8314 (tt) outliers start: 44 outliers final: 22 residues processed: 275 average time/residue: 0.7715 time to fit residues: 238.5715 Evaluate side-chains 270 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 55 VAL 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 2 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 171 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 201 optimal weight: 0.7980 chunk 214 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 218 optimal weight: 0.0870 chunk 157 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 185 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.0962 ------------------------------------------------------------------------------- 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 72 ASN F 195 GLN G 178 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.164866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.136552 restraints weight = 17844.095| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.75 r_work: 0.3178 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work: 0.2910 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23947 Z= 0.122 Angle : 0.530 9.338 32704 Z= 0.286 Chirality : 0.046 0.140 3409 Planarity : 0.004 0.033 4263 Dihedral : 6.245 77.712 3248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.93 % Allowed : 10.87 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.14), residues: 2940 helix: 1.33 (0.23), residues: 504 sheet: 1.35 (0.14), residues: 1036 loop : -0.08 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 288 TYR 0.011 0.002 TYR G 304 PHE 0.021 0.002 PHE E 321 TRP 0.014 0.001 TRP G 373 HIS 0.004 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00254 (23933) covalent geometry : angle 0.52943 (32676) SS BOND : bond 0.00193 ( 14) SS BOND : angle 0.71683 ( 28) hydrogen bonds : bond 0.04125 ( 880) hydrogen bonds : angle 5.10655 ( 2481) *********************** 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 289 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 241 time to evaluate : 1.060 Fit side-chains REVERT: A 385 MET cc_start: 0.9060 (mmm) cc_final: 0.8767 (mmm) REVERT: B 2 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: B 8 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: B 277 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8234 (tt) REVERT: B 378 GLN cc_start: 0.8091 (tt0) cc_final: 0.7784 (tm-30) REVERT: C 8 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: D 57 MET cc_start: 0.7021 (mtp) cc_final: 0.6745 (mtp) REVERT: E 8 GLN cc_start: 0.7658 (mt0) cc_final: 0.7396 (mt0) REVERT: E 171 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8574 (mptt) REVERT: F 29 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: F 258 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: F 277 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8527 (tt) REVERT: G 29 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: G 258 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: G 277 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8314 (tt) outliers start: 48 outliers final: 26 residues processed: 281 average time/residue: 0.7870 time to fit residues: 248.3839 Evaluate side-chains 276 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 GLU 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 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 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 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 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 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 159 optimal weight: 0.0170 chunk 278 optimal weight: 7.9990 chunk 176 optimal weight: 0.0020 chunk 149 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 172 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 overall best weight: 0.4826 ------------------------------------------------------------------------------- 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 A 341 HIS B 195 GLN C 174 ASN C 178 ASN D 72 ASN E 72 ASN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 8 GLN G 178 ASN G 341 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.168351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140764 restraints weight = 17940.798| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 0.73 r_work: 0.3241 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23947 Z= 0.077 Angle : 0.450 7.293 32704 Z= 0.240 Chirality : 0.044 0.139 3409 Planarity : 0.003 0.031 4263 Dihedral : 5.697 71.669 3248 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.32 % Allowed : 11.48 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.15), residues: 2940 helix: 1.61 (0.23), residues: 504 sheet: 1.52 (0.14), residues: 1008 loop : 0.16 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 397 TYR 0.009 0.001 TYR D 330 PHE 0.010 0.001 PHE C 321 TRP 0.011 0.001 TRP B 373 HIS 0.002 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00159 (23933) covalent geometry : angle 0.45005 (32676) SS BOND : bond 0.00195 ( 14) SS BOND : angle 0.48871 ( 28) hydrogen bonds : bond 0.02751 ( 880) hydrogen bonds : angle 4.77909 ( 2481) *********************** 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 281 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 0.973 Fit side-chains REVERT: A 242 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8057 (tttm) REVERT: B 288 ARG cc_start: 0.8674 (mmt180) cc_final: 0.8405 (mmm160) REVERT: B 378 GLN cc_start: 0.7978 (tt0) cc_final: 0.7724 (tm-30) REVERT: C 8 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: D 57 MET cc_start: 0.7039 (mtp) cc_final: 0.6775 (mtp) REVERT: E 8 GLN cc_start: 0.7558 (mt0) cc_final: 0.7331 (mt0) REVERT: E 171 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8432 (mptt) REVERT: F 2 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: F 29 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: G 29 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6255 (mm-30) REVERT: G 254 GLU cc_start: 0.7514 (tt0) cc_final: 0.7302 (tt0) outliers start: 33 outliers final: 18 residues processed: 273 average time/residue: 0.7559 time to fit residues: 232.1414 Evaluate side-chains 258 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain C residue 408 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 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 171 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain G residue 29 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 167 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 chunk 278 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 224 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 132 HIS 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 = 0.3767 r_free = 0.3767 target = 0.164224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135942 restraints weight = 17628.303| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.73 r_work: 0.3167 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work: 0.2900 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23947 Z= 0.167 Angle : 0.587 10.862 32704 Z= 0.317 Chirality : 0.048 0.166 3409 Planarity : 0.004 0.032 4263 Dihedral : 6.098 74.431 3245 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 11.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 2940 helix: 1.34 (0.23), residues: 504 sheet: 1.40 (0.14), residues: 1001 loop : 0.03 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 391 TYR 0.013 0.002 TYR C 357 PHE 0.025 0.003 PHE E 321 TRP 0.017 0.002 TRP D 329 HIS 0.006 0.002 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00353 (23933) covalent geometry : angle 0.58690 (32676) SS BOND : bond 0.00282 ( 14) SS BOND : angle 0.90851 ( 28) hydrogen bonds : bond 0.04872 ( 880) hydrogen bonds : angle 5.19141 ( 2481) *********************** 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 279 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 1.006 Fit side-chains REVERT: A 385 MET cc_start: 0.9019 (mmm) cc_final: 0.8699 (mmm) REVERT: B 2 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7337 (mm-30) REVERT: B 277 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 378 GLN cc_start: 0.8056 (tt0) cc_final: 0.7738 (tm-30) REVERT: C 8 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: D 57 MET cc_start: 0.6927 (mtp) cc_final: 0.6678 (mtp) REVERT: E 171 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8583 (mptt) REVERT: F 2 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: F 29 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5971 (tm-30) REVERT: F 277 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8569 (tt) REVERT: G 29 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6148 (tm-30) REVERT: G 277 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8378 (tt) outliers start: 44 outliers final: 26 residues processed: 269 average time/residue: 0.7475 time to fit residues: 225.9459 Evaluate side-chains 272 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 2 GLU 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 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 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 171 LYS Chi-restraints excluded: chain F residue 249 LEU 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 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 121 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135917 restraints weight = 17740.858| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.74 r_work: 0.3159 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work: 0.2889 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23947 Z= 0.175 Angle : 0.604 11.068 32704 Z= 0.328 Chirality : 0.048 0.186 3409 Planarity : 0.004 0.033 4263 Dihedral : 6.215 73.560 3245 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 11.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.14), residues: 2940 helix: 1.18 (0.23), residues: 504 sheet: 1.38 (0.14), residues: 994 loop : -0.12 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 391 TYR 0.014 0.002 TYR C 357 PHE 0.027 0.003 PHE C 321 TRP 0.015 0.002 TRP E 373 HIS 0.007 0.002 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00371 (23933) covalent geometry : angle 0.60355 (32676) SS BOND : bond 0.00279 ( 14) SS BOND : angle 0.95117 ( 28) hydrogen bonds : bond 0.05024 ( 880) hydrogen bonds : angle 5.28567 ( 2481) *********************** 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 278 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 0.744 Fit side-chains REVERT: A 8 GLN cc_start: 0.7579 (mt0) cc_final: 0.7345 (mt0) REVERT: A 385 MET cc_start: 0.9043 (mmm) cc_final: 0.8697 (mmm) REVERT: B 277 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 378 GLN cc_start: 0.8117 (tt0) cc_final: 0.7779 (tm-30) REVERT: C 8 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: D 2 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: D 57 MET cc_start: 0.7024 (mtp) cc_final: 0.6686 (mtp) REVERT: E 171 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8666 (mptt) REVERT: F 2 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: F 29 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6029 (tm-30) REVERT: F 277 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8611 (tt) REVERT: G 8 GLN cc_start: 0.7571 (mt0) cc_final: 0.7336 (mt0) REVERT: G 29 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6174 (tm-30) REVERT: G 258 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: G 277 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8396 (tt) outliers start: 41 outliers final: 25 residues processed: 270 average time/residue: 0.7502 time to fit residues: 227.9446 Evaluate side-chains 272 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 135 optimal weight: 0.6980 chunk 101 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 208 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 132 HIS G 178 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.165486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138255 restraints weight = 18018.601| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.72 r_work: 0.3202 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work: 0.2923 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23947 Z= 0.102 Angle : 0.503 8.389 32704 Z= 0.270 Chirality : 0.045 0.139 3409 Planarity : 0.003 0.032 4263 Dihedral : 5.850 69.383 3245 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.24 % Allowed : 11.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.14), residues: 2940 helix: 1.41 (0.23), residues: 504 sheet: 1.37 (0.14), residues: 1036 loop : -0.06 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 288 TYR 0.010 0.001 TYR C 304 PHE 0.019 0.002 PHE E 321 TRP 0.013 0.001 TRP B 373 HIS 0.003 0.001 HIS C 341 Details of bonding type rmsd covalent geometry : bond 0.00210 (23933) covalent geometry : angle 0.50270 (32676) SS BOND : bond 0.00141 ( 14) SS BOND : angle 0.66130 ( 28) hydrogen bonds : bond 0.03659 ( 880) hydrogen bonds : angle 5.01232 ( 2481) ********************** 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: 31 poor density : 240 time to evaluate : 1.012 Fit side-chains REVERT: A 385 MET cc_start: 0.8987 (mmm) cc_final: 0.8541 (mmm) REVERT: B 277 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8161 (tt) REVERT: B 378 GLN cc_start: 0.8055 (tt0) cc_final: 0.7744 (tm-30) REVERT: C 8 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: D 2 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: D 57 MET cc_start: 0.6900 (mtp) cc_final: 0.6623 (mtp) REVERT: E 171 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8493 (mptt) REVERT: F 2 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: F 29 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6098 (mm-30) REVERT: G 277 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8277 (tt) REVERT: G 350 ASP cc_start: 0.9032 (p0) cc_final: 0.8819 (p0) outliers start: 31 outliers final: 21 residues processed: 264 average time/residue: 0.7584 time to fit residues: 225.0019 Evaluate side-chains 265 residues out of total 2492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 8 GLN Chi-restraints excluded: chain C residue 55 VAL 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 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 408 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 289 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 79 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 132 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 overall best weight: 3.5564 ------------------------------------------------------------------------------- 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 178 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.165155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136901 restraints weight = 17724.331| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.75 r_work: 0.3210 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23947 Z= 0.172 Angle : 0.598 10.900 32704 Z= 0.324 Chirality : 0.048 0.170 3409 Planarity : 0.004 0.033 4263 Dihedral : 6.159 70.092 3245 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.40 % Allowed : 11.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.14), residues: 2940 helix: 1.23 (0.23), residues: 504 sheet: 1.37 (0.14), residues: 1001 loop : -0.06 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 391 TYR 0.013 0.002 TYR C 357 PHE 0.026 0.003 PHE E 321 TRP 0.015 0.002 TRP A 370 HIS 0.006 0.002 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00366 (23933) covalent geometry : angle 0.59789 (32676) SS BOND : bond 0.00267 ( 14) SS BOND : angle 0.91320 ( 28) hydrogen bonds : bond 0.04977 ( 880) hydrogen bonds : angle 5.26127 ( 2481) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12669.07 seconds wall clock time: 215 minutes 12.91 seconds (12912.91 seconds total)