Starting phenix.real_space_refine on Mon Jul 28 13:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.map" model { file = "/net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye3_39188/07_2025/8ye3_39188.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.040 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 66 5.16 5 C 6627 2.51 5 N 1725 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10491 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3497 Classifications: {'peptide': 452} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 438} Chain breaks: 1 Restraints were copied for chains: C, B Time building chain proxies: 6.76, per 1000 atoms: 0.64 Number of scatterers: 10491 At special positions: 0 Unit cell: (92.112, 89.688, 122.816, 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 66 16.00 O 2073 8.00 N 1725 7.00 C 6627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " 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: 3.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 35.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 removed outlier: 3.596A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 195 through 203 removed outlier: 4.137A pdb=" N LYS A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.302A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.213A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 513 Processing helix chain 'B' and resid 73 through 96 removed outlier: 3.597A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.137A pdb=" N LYS B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 216 through 226 removed outlier: 4.302A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.214A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'C' and resid 73 through 96 removed outlier: 3.597A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.136A pdb=" N LYS C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 Processing helix chain 'C' and resid 216 through 226 removed outlier: 4.303A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 4.213A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.582A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.503A pdb=" N PHE C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 513 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR A 29 " --> pdb=" O LYS A 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 186 through 194 current: chain 'A' and resid 286 through 293 removed outlier: 7.088A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 349 through 352 current: chain 'A' and resid 364 through 368 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA3, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.597A pdb=" N GLY A 411 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 442 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.209A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 449 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR B 29 " --> pdb=" O LYS B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 186 through 194 current: chain 'B' and resid 286 through 293 removed outlier: 7.087A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 349 through 352 current: chain 'B' and resid 364 through 368 Processing sheet with id=AA6, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AA7, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.597A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 442 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.208A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 449 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 33 removed outlier: 5.709A pdb=" N THR C 29 " --> pdb=" O LYS C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 186 through 194 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 186 through 194 current: chain 'C' and resid 286 through 293 removed outlier: 7.087A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 349 through 352 current: chain 'C' and resid 364 through 368 Processing sheet with id=AB1, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.598A pdb=" N GLY C 411 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 442 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 430 through 434 removed outlier: 5.209A pdb=" N ILE C 431 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASN C 426 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C 449 " --> pdb=" O SER C 425 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1125 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: 4.06 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3369 1.35 - 1.46: 2329 1.46 - 1.58: 4853 1.58 - 1.70: 3 1.70 - 1.82: 90 Bond restraints: 10644 Sorted by residual: bond pdb=" CB PRO B 101 " pdb=" CG PRO B 101 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.68e+00 bond pdb=" CB PRO A 101 " pdb=" CG PRO A 101 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.64e+00 bond pdb=" CB PRO C 101 " pdb=" CG PRO C 101 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.62e+00 bond pdb=" CG PRO C 265 " pdb=" CD PRO C 265 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.37e+00 bond pdb=" CG PRO B 265 " pdb=" CD PRO B 265 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.31e+00 ... (remaining 10639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 14249 2.08 - 4.16: 136 4.16 - 6.24: 33 6.24 - 8.32: 0 8.32 - 10.40: 3 Bond angle restraints: 14421 Sorted by residual: angle pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 112.00 106.11 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" CA PRO B 265 " pdb=" N PRO B 265 " pdb=" CD PRO B 265 " ideal model delta sigma weight residual 112.00 106.11 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" CA PRO C 265 " pdb=" N PRO C 265 " pdb=" CD PRO C 265 " ideal model delta sigma weight residual 112.00 106.13 5.87 1.40e+00 5.10e-01 1.76e+01 angle pdb=" CA PRO B 101 " pdb=" N PRO B 101 " pdb=" CD PRO B 101 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 angle pdb=" CA PRO C 101 " pdb=" N PRO C 101 " pdb=" CD PRO C 101 " ideal model delta sigma weight residual 112.00 106.59 5.41 1.40e+00 5.10e-01 1.49e+01 ... (remaining 14416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5526 17.66 - 35.33: 740 35.33 - 52.99: 258 52.99 - 70.66: 40 70.66 - 88.32: 15 Dihedral angle restraints: 6579 sinusoidal: 2598 harmonic: 3981 Sorted by residual: dihedral pdb=" CB CYS C 416 " pdb=" SG CYS C 416 " pdb=" SG CYS C 422 " pdb=" CB CYS C 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.78 70.78 1 1.00e+01 1.00e-02 6.44e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.74 70.74 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 422 " pdb=" CB CYS B 422 " ideal model delta sinusoidal sigma weight residual -86.00 -156.73 70.73 1 1.00e+01 1.00e-02 6.43e+01 ... (remaining 6576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1489 0.058 - 0.116: 238 0.116 - 0.173: 13 0.173 - 0.231: 0 0.231 - 0.289: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB ILE B 292 " pdb=" CA ILE B 292 " pdb=" CG1 ILE B 292 " pdb=" CG2 ILE B 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE C 292 " pdb=" CA ILE C 292 " pdb=" CG1 ILE C 292 " pdb=" CG2 ILE C 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE A 292 " pdb=" CA ILE A 292 " pdb=" CG1 ILE A 292 " pdb=" CG2 ILE A 292 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1740 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 264 " 0.059 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO C 265 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 264 " -0.059 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 265 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 265 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 265 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 264 " -0.059 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO A 265 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.047 5.00e-02 4.00e+02 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 277 2.69 - 3.24: 9963 3.24 - 3.80: 16167 3.80 - 4.35: 20986 4.35 - 4.90: 35406 Nonbonded interactions: 82799 Sorted by model distance: nonbonded pdb=" OG1 THR A 36 " pdb=" OG SER A 38 " model vdw 2.140 3.040 nonbonded pdb=" OG1 THR B 36 " pdb=" OG SER B 38 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR C 36 " pdb=" OG SER C 38 " model vdw 2.141 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OD1 ASN B 331 " model vdw 2.194 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OD1 ASN A 331 " model vdw 2.194 3.040 ... (remaining 82794 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 288.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.070 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 322.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 0.108 10665 Z= 0.118 Angle : 0.534 10.396 14463 Z= 0.285 Chirality : 0.042 0.289 1743 Planarity : 0.005 0.087 1812 Dihedral : 17.687 88.319 3936 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.89 % Allowed : 31.88 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.23), residues: 1344 helix: 0.68 (0.26), residues: 435 sheet: 0.22 (0.29), residues: 333 loop : -1.11 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 52 HIS 0.001 0.000 HIS B 317 PHE 0.011 0.001 PHE B 351 TYR 0.014 0.001 TYR A 417 ARG 0.004 0.000 ARG B 507 Details of bonding type rmsd hydrogen bonds : bond 0.18257 ( 411) hydrogen bonds : angle 7.07384 ( 1125) SS BOND : bond 0.00159 ( 21) SS BOND : angle 0.73609 ( 42) covalent geometry : bond 0.00329 (10644) covalent geometry : angle 0.53379 (14421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 352 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 338 ASP cc_start: 0.7102 (p0) cc_final: 0.6800 (p0) REVERT: A 370 MET cc_start: 0.8408 (ttm) cc_final: 0.8129 (ttm) REVERT: A 444 ASN cc_start: 0.7834 (p0) cc_final: 0.7107 (p0) REVERT: A 445 LYS cc_start: 0.7024 (mmtm) cc_final: 0.6768 (mmtm) REVERT: B 163 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6253 (mm-30) REVERT: B 236 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 238 SER cc_start: 0.7773 (t) cc_final: 0.7202 (m) REVERT: B 259 SER cc_start: 0.7724 (t) cc_final: 0.7305 (p) REVERT: B 263 ASP cc_start: 0.7149 (m-30) cc_final: 0.6894 (m-30) REVERT: B 272 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7466 (ttpp) REVERT: B 293 LYS cc_start: 0.7425 (mtpp) cc_final: 0.6982 (mtmm) REVERT: B 338 ASP cc_start: 0.7057 (p0) cc_final: 0.6621 (p0) REVERT: B 357 THR cc_start: 0.7595 (p) cc_final: 0.7285 (t) REVERT: B 399 LYS cc_start: 0.7350 (pttm) cc_final: 0.7093 (pttm) REVERT: B 414 VAL cc_start: 0.7865 (t) cc_final: 0.7462 (p) REVERT: B 488 PHE cc_start: 0.7885 (t80) cc_final: 0.7547 (t80) REVERT: C 351 PHE cc_start: 0.8043 (t80) cc_final: 0.7820 (t80) REVERT: C 357 THR cc_start: 0.7759 (p) cc_final: 0.7444 (t) outliers start: 11 outliers final: 10 residues processed: 353 average time/residue: 0.2628 time to fit residues: 132.2058 Evaluate side-chains 342 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 332 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 508 LYS Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 302 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 224 GLN B 225 GLN B 270 GLN B 302 GLN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.109924 restraints weight = 14720.703| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.12 r_work: 0.3178 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10665 Z= 0.224 Angle : 0.606 8.195 14463 Z= 0.314 Chirality : 0.044 0.227 1743 Planarity : 0.004 0.026 1812 Dihedral : 5.608 57.856 1454 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.58 % Allowed : 27.35 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1344 helix: 0.90 (0.26), residues: 432 sheet: 0.42 (0.28), residues: 357 loop : -1.15 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 314 HIS 0.006 0.002 HIS C 317 PHE 0.018 0.002 PHE C 32 TYR 0.016 0.002 TYR A 342 ARG 0.003 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 411) hydrogen bonds : angle 5.28011 ( 1125) SS BOND : bond 0.00450 ( 21) SS BOND : angle 1.04610 ( 42) covalent geometry : bond 0.00509 (10644) covalent geometry : angle 0.60446 (14421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7374 (tt0) cc_final: 0.7095 (tt0) REVERT: A 82 GLU cc_start: 0.7983 (tp30) cc_final: 0.7660 (tp30) REVERT: A 146 SER cc_start: 0.8252 (t) cc_final: 0.7994 (t) REVERT: A 152 VAL cc_start: 0.8796 (m) cc_final: 0.8456 (t) REVERT: A 166 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8496 (mtpt) REVERT: A 198 TYR cc_start: 0.8490 (t80) cc_final: 0.8169 (t80) REVERT: A 218 GLU cc_start: 0.8020 (mp0) cc_final: 0.7603 (mp0) REVERT: A 236 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 289 MET cc_start: 0.8139 (mmm) cc_final: 0.7852 (tmm) REVERT: A 318 THR cc_start: 0.8621 (m) cc_final: 0.8397 (p) REVERT: A 378 GLU cc_start: 0.8154 (mp0) cc_final: 0.7947 (mp0) REVERT: A 494 GLN cc_start: 0.8117 (mt0) cc_final: 0.7860 (mt0) REVERT: B 82 GLU cc_start: 0.8035 (tp30) cc_final: 0.7773 (tp30) REVERT: B 160 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7402 (mm) REVERT: B 163 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6219 (mm-30) REVERT: B 166 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8343 (mtpt) REVERT: B 174 THR cc_start: 0.7996 (t) cc_final: 0.7687 (p) REVERT: B 232 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: B 236 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 238 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 289 MET cc_start: 0.8226 (mmm) cc_final: 0.8000 (tpp) REVERT: B 338 ASP cc_start: 0.7258 (p0) cc_final: 0.6954 (p0) REVERT: B 421 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8115 (mmpt) REVERT: B 444 ASN cc_start: 0.8122 (p0) cc_final: 0.7895 (p0) REVERT: C 34 GLN cc_start: 0.8699 (tt0) cc_final: 0.8456 (tt0) REVERT: C 82 GLU cc_start: 0.7905 (tp30) cc_final: 0.7663 (tp30) REVERT: C 171 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8338 (mp) REVERT: C 222 GLU cc_start: 0.7987 (tp30) cc_final: 0.7499 (tp30) REVERT: C 289 MET cc_start: 0.8207 (mmm) cc_final: 0.7867 (tmm) REVERT: C 338 ASP cc_start: 0.7142 (p0) cc_final: 0.6770 (p0) REVERT: C 343 CYS cc_start: 0.7442 (m) cc_final: 0.7200 (m) REVERT: C 478 TYR cc_start: 0.7968 (m-10) cc_final: 0.7735 (m-10) outliers start: 69 outliers final: 29 residues processed: 397 average time/residue: 0.2547 time to fit residues: 144.3539 Evaluate side-chains 397 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 363 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 302 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111408 restraints weight = 14471.736| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.01 r_work: 0.3130 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10665 Z= 0.216 Angle : 0.586 7.504 14463 Z= 0.303 Chirality : 0.044 0.256 1743 Planarity : 0.003 0.031 1812 Dihedral : 4.616 47.525 1431 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.34 % Allowed : 28.96 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1344 helix: 1.10 (0.26), residues: 414 sheet: 0.38 (0.29), residues: 327 loop : -1.24 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS B 317 PHE 0.030 0.002 PHE A 509 TYR 0.013 0.002 TYR A 342 ARG 0.004 0.000 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 411) hydrogen bonds : angle 5.18124 ( 1125) SS BOND : bond 0.00490 ( 21) SS BOND : angle 1.02843 ( 42) covalent geometry : bond 0.00488 (10644) covalent geometry : angle 0.58399 (14421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 383 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7876 (tp30) cc_final: 0.7667 (tp30) REVERT: A 152 VAL cc_start: 0.8805 (m) cc_final: 0.8426 (t) REVERT: A 218 GLU cc_start: 0.7928 (mp0) cc_final: 0.7568 (mp0) REVERT: A 222 GLU cc_start: 0.7810 (tp30) cc_final: 0.7320 (tp30) REVERT: A 225 GLN cc_start: 0.8167 (mt0) cc_final: 0.7959 (mt0) REVERT: A 232 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 236 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 289 MET cc_start: 0.8232 (mmm) cc_final: 0.7953 (tpp) REVERT: A 454 ASN cc_start: 0.8012 (m-40) cc_final: 0.7775 (m-40) REVERT: B 38 SER cc_start: 0.8620 (p) cc_final: 0.8390 (p) REVERT: B 78 LEU cc_start: 0.8463 (mt) cc_final: 0.8152 (mp) REVERT: B 82 GLU cc_start: 0.7901 (tp30) cc_final: 0.7672 (tp30) REVERT: B 160 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7387 (mm) REVERT: B 163 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6261 (mm-30) REVERT: B 174 THR cc_start: 0.8129 (t) cc_final: 0.7918 (p) REVERT: B 236 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 238 SER cc_start: 0.8657 (t) cc_final: 0.8268 (p) REVERT: B 289 MET cc_start: 0.8195 (tmm) cc_final: 0.7860 (tmm) REVERT: B 296 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 338 ASP cc_start: 0.7261 (p0) cc_final: 0.6936 (p0) REVERT: B 405 SER cc_start: 0.8630 (p) cc_final: 0.8404 (p) REVERT: C 34 GLN cc_start: 0.8776 (tt0) cc_final: 0.8474 (tt0) REVERT: C 42 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7592 (mtmm) REVERT: C 82 GLU cc_start: 0.7776 (tp30) cc_final: 0.7568 (tp30) REVERT: C 163 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6460 (mm-30) REVERT: C 174 THR cc_start: 0.8422 (t) cc_final: 0.8194 (p) REVERT: C 222 GLU cc_start: 0.7912 (tp30) cc_final: 0.7293 (tp30) REVERT: C 236 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 251 MET cc_start: 0.8109 (mtt) cc_final: 0.7804 (mtp) REVERT: C 263 ASP cc_start: 0.7688 (m-30) cc_final: 0.7487 (m-30) REVERT: C 338 ASP cc_start: 0.7127 (p0) cc_final: 0.6806 (p0) REVERT: C 343 CYS cc_start: 0.7491 (m) cc_final: 0.7235 (m) REVERT: C 393 CYS cc_start: 0.7498 (m) cc_final: 0.7258 (m) REVERT: C 509 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6728 (m-80) outliers start: 66 outliers final: 36 residues processed: 407 average time/residue: 0.2012 time to fit residues: 117.0161 Evaluate side-chains 409 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 0.0770 chunk 94 optimal weight: 0.0020 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.3746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 345 ASN B 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114700 restraints weight = 14424.119| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.05 r_work: 0.3214 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10665 Z= 0.098 Angle : 0.499 7.031 14463 Z= 0.258 Chirality : 0.041 0.236 1743 Planarity : 0.003 0.025 1812 Dihedral : 4.191 41.319 1431 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.53 % Allowed : 28.96 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1344 helix: 1.40 (0.27), residues: 414 sheet: 0.41 (0.29), residues: 324 loop : -1.14 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 314 HIS 0.001 0.000 HIS B 317 PHE 0.027 0.001 PHE A 32 TYR 0.013 0.001 TYR B 417 ARG 0.001 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 411) hydrogen bonds : angle 4.86910 ( 1125) SS BOND : bond 0.00283 ( 21) SS BOND : angle 0.98629 ( 42) covalent geometry : bond 0.00223 (10644) covalent geometry : angle 0.49639 (14421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 359 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8527 (t80) cc_final: 0.8270 (t80) REVERT: A 40 VAL cc_start: 0.8272 (m) cc_final: 0.8064 (t) REVERT: A 82 GLU cc_start: 0.7861 (tp30) cc_final: 0.7657 (tp30) REVERT: A 152 VAL cc_start: 0.8746 (m) cc_final: 0.8356 (t) REVERT: A 163 GLU cc_start: 0.6445 (mm-30) cc_final: 0.6214 (mm-30) REVERT: A 232 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 236 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 289 MET cc_start: 0.8031 (tmm) cc_final: 0.7807 (tpp) REVERT: A 454 ASN cc_start: 0.8096 (m-40) cc_final: 0.7829 (m-40) REVERT: A 461 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8126 (mmtt) REVERT: B 38 SER cc_start: 0.8529 (p) cc_final: 0.8310 (m) REVERT: B 160 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7288 (mm) REVERT: B 163 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6170 (mm-30) REVERT: B 174 THR cc_start: 0.8077 (t) cc_final: 0.7839 (p) REVERT: B 222 GLU cc_start: 0.7947 (tp30) cc_final: 0.7744 (tt0) REVERT: B 236 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 238 SER cc_start: 0.8514 (t) cc_final: 0.8164 (p) REVERT: B 296 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7853 (m) REVERT: B 338 ASP cc_start: 0.7146 (p0) cc_final: 0.6837 (p0) REVERT: C 34 GLN cc_start: 0.8696 (tt0) cc_final: 0.8409 (tt0) REVERT: C 42 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7463 (mtmm) REVERT: C 82 GLU cc_start: 0.7753 (tp30) cc_final: 0.7543 (tp30) REVERT: C 163 GLU cc_start: 0.6584 (mm-30) cc_final: 0.6349 (mm-30) REVERT: C 174 THR cc_start: 0.8354 (t) cc_final: 0.8080 (p) REVERT: C 222 GLU cc_start: 0.7868 (tp30) cc_final: 0.7355 (tp30) REVERT: C 236 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 251 MET cc_start: 0.7947 (mtt) cc_final: 0.7717 (mtp) REVERT: C 289 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: C 338 ASP cc_start: 0.7078 (p0) cc_final: 0.6663 (p0) REVERT: C 361 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: C 393 CYS cc_start: 0.7520 (m) cc_final: 0.7289 (m) REVERT: C 399 LYS cc_start: 0.7885 (pttm) cc_final: 0.7370 (pttm) REVERT: C 454 ASN cc_start: 0.8004 (m-40) cc_final: 0.7694 (m-40) outliers start: 56 outliers final: 38 residues processed: 378 average time/residue: 0.2059 time to fit residues: 111.4284 Evaluate side-chains 395 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 352 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 225 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 224 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 240 ASN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112200 restraints weight = 14330.354| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.03 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10665 Z= 0.170 Angle : 0.551 6.864 14463 Z= 0.284 Chirality : 0.043 0.322 1743 Planarity : 0.003 0.028 1812 Dihedral : 4.124 17.818 1428 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.07 % Allowed : 28.24 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1344 helix: 1.42 (0.27), residues: 414 sheet: 0.38 (0.29), residues: 327 loop : -1.14 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.003 0.001 HIS A 317 PHE 0.026 0.001 PHE C 509 TYR 0.011 0.001 TYR A 299 ARG 0.001 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 411) hydrogen bonds : angle 4.90879 ( 1125) SS BOND : bond 0.00416 ( 21) SS BOND : angle 1.24619 ( 42) covalent geometry : bond 0.00388 (10644) covalent geometry : angle 0.54771 (14421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 365 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8421 (m) cc_final: 0.8158 (t) REVERT: A 82 GLU cc_start: 0.7853 (tp30) cc_final: 0.7563 (tp30) REVERT: A 152 VAL cc_start: 0.8794 (m) cc_final: 0.8434 (t) REVERT: A 163 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 218 GLU cc_start: 0.8046 (mp0) cc_final: 0.7567 (mp0) REVERT: A 222 GLU cc_start: 0.7798 (tp30) cc_final: 0.7254 (tp30) REVERT: A 232 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: A 289 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7909 (tpp) REVERT: A 378 GLU cc_start: 0.8222 (mp0) cc_final: 0.8007 (mp0) REVERT: A 454 ASN cc_start: 0.7988 (m-40) cc_final: 0.7729 (m110) REVERT: A 461 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8067 (mmtt) REVERT: B 38 SER cc_start: 0.8584 (p) cc_final: 0.8318 (m) REVERT: B 160 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 163 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6207 (mm-30) REVERT: B 174 THR cc_start: 0.8063 (t) cc_final: 0.7830 (p) REVERT: B 236 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7357 (mt-10) REVERT: B 238 SER cc_start: 0.8575 (t) cc_final: 0.8230 (p) REVERT: B 296 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7955 (m) REVERT: B 308 VAL cc_start: 0.8872 (t) cc_final: 0.8626 (t) REVERT: B 338 ASP cc_start: 0.7203 (p0) cc_final: 0.6912 (p0) REVERT: C 34 GLN cc_start: 0.8756 (tt0) cc_final: 0.8460 (tt0) REVERT: C 42 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7527 (mtmm) REVERT: C 82 GLU cc_start: 0.7829 (tp30) cc_final: 0.7621 (tp30) REVERT: C 163 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6406 (mm-30) REVERT: C 174 THR cc_start: 0.8290 (t) cc_final: 0.8046 (p) REVERT: C 222 GLU cc_start: 0.7942 (tp30) cc_final: 0.7408 (tp30) REVERT: C 225 GLN cc_start: 0.8005 (mt0) cc_final: 0.7715 (mt0) REVERT: C 236 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 289 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7715 (tmm) REVERT: C 338 ASP cc_start: 0.7097 (p0) cc_final: 0.6664 (p0) REVERT: C 351 PHE cc_start: 0.8460 (t80) cc_final: 0.8111 (t80) REVERT: C 361 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: C 393 CYS cc_start: 0.7513 (m) cc_final: 0.7268 (m) REVERT: C 399 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7690 (pttm) REVERT: C 454 ASN cc_start: 0.7995 (m-40) cc_final: 0.7718 (m-40) REVERT: C 494 GLN cc_start: 0.8229 (mt0) cc_final: 0.7966 (mt0) outliers start: 75 outliers final: 51 residues processed: 396 average time/residue: 0.2076 time to fit residues: 118.1308 Evaluate side-chains 435 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 377 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 116 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 225 GLN B 224 GLN B 270 GLN B 345 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113489 restraints weight = 14535.298| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.06 r_work: 0.3223 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10665 Z= 0.123 Angle : 0.515 6.800 14463 Z= 0.267 Chirality : 0.042 0.326 1743 Planarity : 0.003 0.022 1812 Dihedral : 4.010 18.037 1428 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.50 % Allowed : 28.96 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1344 helix: 1.27 (0.26), residues: 432 sheet: 0.40 (0.29), residues: 327 loop : -1.11 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 314 HIS 0.002 0.001 HIS A 317 PHE 0.028 0.001 PHE A 32 TYR 0.010 0.001 TYR A 417 ARG 0.001 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 411) hydrogen bonds : angle 4.85557 ( 1125) SS BOND : bond 0.00286 ( 21) SS BOND : angle 1.18139 ( 42) covalent geometry : bond 0.00284 (10644) covalent geometry : angle 0.51226 (14421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 361 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8716 (m) cc_final: 0.8418 (p) REVERT: A 82 GLU cc_start: 0.7863 (tp30) cc_final: 0.7622 (tp30) REVERT: A 152 VAL cc_start: 0.8756 (m) cc_final: 0.8386 (t) REVERT: A 163 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6201 (mm-30) REVERT: A 218 GLU cc_start: 0.8025 (mp0) cc_final: 0.7606 (mp0) REVERT: A 226 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7907 (mmmm) REVERT: A 232 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 289 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7851 (tmm) REVERT: A 378 GLU cc_start: 0.8212 (mp0) cc_final: 0.8004 (mp0) REVERT: A 433 LYS cc_start: 0.8444 (tttm) cc_final: 0.8230 (tttm) REVERT: A 454 ASN cc_start: 0.8008 (m-40) cc_final: 0.7761 (m110) REVERT: B 38 SER cc_start: 0.8540 (p) cc_final: 0.8323 (m) REVERT: B 160 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7304 (mm) REVERT: B 163 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6170 (mm-30) REVERT: B 174 THR cc_start: 0.8071 (t) cc_final: 0.7842 (p) REVERT: B 236 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 238 SER cc_start: 0.8546 (t) cc_final: 0.8221 (p) REVERT: B 289 MET cc_start: 0.8033 (mmm) cc_final: 0.7793 (tmm) REVERT: B 308 VAL cc_start: 0.8854 (t) cc_final: 0.8626 (t) REVERT: C 34 GLN cc_start: 0.8764 (tt0) cc_final: 0.8471 (tt0) REVERT: C 42 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7421 (mtmm) REVERT: C 82 GLU cc_start: 0.7819 (tp30) cc_final: 0.7609 (tp30) REVERT: C 163 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6412 (mm-30) REVERT: C 174 THR cc_start: 0.8244 (t) cc_final: 0.8036 (p) REVERT: C 222 GLU cc_start: 0.7914 (tp30) cc_final: 0.7378 (tp30) REVERT: C 236 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 289 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: C 338 ASP cc_start: 0.7059 (p0) cc_final: 0.6658 (p0) REVERT: C 361 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: C 393 CYS cc_start: 0.7553 (m) cc_final: 0.7303 (m) REVERT: C 399 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7617 (pttm) REVERT: C 494 GLN cc_start: 0.8186 (mt0) cc_final: 0.7948 (mt0) outliers start: 68 outliers final: 52 residues processed: 386 average time/residue: 0.2172 time to fit residues: 117.7984 Evaluate side-chains 414 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 356 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 119 optimal weight: 0.0470 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 270 GLN B 454 ASN C 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112849 restraints weight = 14517.896| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.05 r_work: 0.3220 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10665 Z= 0.145 Angle : 0.528 6.531 14463 Z= 0.273 Chirality : 0.042 0.369 1743 Planarity : 0.003 0.024 1812 Dihedral : 4.047 17.863 1428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.39 % Allowed : 27.91 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1344 helix: 1.25 (0.26), residues: 432 sheet: 0.34 (0.29), residues: 327 loop : -1.11 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.023 0.001 PHE A 32 TYR 0.010 0.001 TYR B 417 ARG 0.002 0.000 ARG B 282 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 411) hydrogen bonds : angle 4.83723 ( 1125) SS BOND : bond 0.00253 ( 21) SS BOND : angle 1.07143 ( 42) covalent geometry : bond 0.00332 (10644) covalent geometry : angle 0.52541 (14421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 364 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8669 (m) cc_final: 0.8378 (p) REVERT: A 82 GLU cc_start: 0.7882 (tp30) cc_final: 0.7628 (tp30) REVERT: A 85 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8225 (mtpp) REVERT: A 152 VAL cc_start: 0.8768 (m) cc_final: 0.8407 (t) REVERT: A 163 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6217 (mm-30) REVERT: A 218 GLU cc_start: 0.7983 (mp0) cc_final: 0.7572 (mp0) REVERT: A 226 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7960 (mmmm) REVERT: A 232 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: A 289 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: A 344 ASP cc_start: 0.7622 (t0) cc_final: 0.7358 (t0) REVERT: A 378 GLU cc_start: 0.8218 (mp0) cc_final: 0.8010 (mp0) REVERT: A 433 LYS cc_start: 0.8451 (tttm) cc_final: 0.8234 (tttm) REVERT: A 454 ASN cc_start: 0.7989 (m-40) cc_final: 0.7780 (m110) REVERT: B 38 SER cc_start: 0.8538 (p) cc_final: 0.8337 (m) REVERT: B 160 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7311 (mm) REVERT: B 174 THR cc_start: 0.8073 (t) cc_final: 0.7850 (p) REVERT: B 236 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7491 (mt-10) REVERT: B 238 SER cc_start: 0.8596 (t) cc_final: 0.8233 (p) REVERT: B 251 MET cc_start: 0.7943 (mtt) cc_final: 0.7743 (mtm) REVERT: B 272 LYS cc_start: 0.7925 (mtpp) cc_final: 0.7563 (ttpp) REVERT: B 289 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7751 (tmm) REVERT: B 308 VAL cc_start: 0.8861 (t) cc_final: 0.8609 (t) REVERT: B 352 PHE cc_start: 0.8394 (m-80) cc_final: 0.8111 (m-80) REVERT: C 34 GLN cc_start: 0.8761 (tt0) cc_final: 0.8464 (tt0) REVERT: C 42 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7403 (mtmm) REVERT: C 222 GLU cc_start: 0.7933 (tp30) cc_final: 0.7416 (tp30) REVERT: C 236 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 289 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: C 338 ASP cc_start: 0.7087 (p0) cc_final: 0.6633 (p0) REVERT: C 343 CYS cc_start: 0.7474 (m) cc_final: 0.7260 (m) REVERT: C 351 PHE cc_start: 0.8467 (t80) cc_final: 0.8123 (t80) REVERT: C 361 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: C 393 CYS cc_start: 0.7589 (m) cc_final: 0.7326 (m) REVERT: C 399 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7618 (pttm) REVERT: C 494 GLN cc_start: 0.8167 (mt0) cc_final: 0.7919 (mt0) outliers start: 79 outliers final: 61 residues processed: 399 average time/residue: 0.2169 time to fit residues: 121.3840 Evaluate side-chains 440 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 372 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110357 restraints weight = 14447.768| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.02 r_work: 0.3184 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10665 Z= 0.191 Angle : 0.566 7.061 14463 Z= 0.293 Chirality : 0.043 0.338 1743 Planarity : 0.003 0.026 1812 Dihedral : 4.249 18.534 1428 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 6.07 % Allowed : 28.07 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1344 helix: 1.16 (0.26), residues: 432 sheet: 0.28 (0.29), residues: 327 loop : -1.15 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.004 0.001 HIS B 317 PHE 0.027 0.001 PHE A 351 TYR 0.014 0.001 TYR B 417 ARG 0.002 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 411) hydrogen bonds : angle 4.95151 ( 1125) SS BOND : bond 0.00402 ( 21) SS BOND : angle 1.20152 ( 42) covalent geometry : bond 0.00436 (10644) covalent geometry : angle 0.56283 (14421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 390 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8656 (m) cc_final: 0.8416 (p) REVERT: A 82 GLU cc_start: 0.7879 (tp30) cc_final: 0.7626 (tp30) REVERT: A 152 VAL cc_start: 0.8790 (m) cc_final: 0.8429 (t) REVERT: A 163 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6220 (mm-30) REVERT: A 222 GLU cc_start: 0.7837 (tp30) cc_final: 0.7369 (tp30) REVERT: A 226 LYS cc_start: 0.8380 (mmmm) cc_final: 0.7920 (mmmm) REVERT: A 232 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 289 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7874 (tmm) REVERT: A 344 ASP cc_start: 0.7697 (t0) cc_final: 0.7462 (t0) REVERT: A 378 GLU cc_start: 0.8217 (mp0) cc_final: 0.7999 (mp0) REVERT: A 393 CYS cc_start: 0.7555 (m) cc_final: 0.7317 (m) REVERT: A 454 ASN cc_start: 0.7925 (m-40) cc_final: 0.7718 (m110) REVERT: B 38 SER cc_start: 0.8577 (p) cc_final: 0.8324 (m) REVERT: B 160 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7301 (mm) REVERT: B 236 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 238 SER cc_start: 0.8655 (OUTLIER) cc_final: 0.8241 (p) REVERT: B 272 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7526 (ttpp) REVERT: B 289 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7804 (tmm) REVERT: B 296 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7972 (m) REVERT: B 361 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: C 34 GLN cc_start: 0.8822 (tt0) cc_final: 0.8547 (tt0) REVERT: C 42 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7387 (mtmm) REVERT: C 201 LYS cc_start: 0.7826 (mtmt) cc_final: 0.7372 (mtmt) REVERT: C 222 GLU cc_start: 0.7921 (tp30) cc_final: 0.7456 (tp30) REVERT: C 236 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 289 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7742 (tmm) REVERT: C 338 ASP cc_start: 0.7093 (p0) cc_final: 0.6689 (p0) REVERT: C 343 CYS cc_start: 0.7516 (m) cc_final: 0.7273 (m) REVERT: C 351 PHE cc_start: 0.8517 (t80) cc_final: 0.8212 (t80) REVERT: C 361 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6844 (tm-30) REVERT: C 393 CYS cc_start: 0.7567 (m) cc_final: 0.7310 (m) REVERT: C 399 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7607 (pttm) outliers start: 75 outliers final: 53 residues processed: 415 average time/residue: 0.2091 time to fit residues: 122.1481 Evaluate side-chains 446 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 383 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 454 ASN C 225 GLN C 345 ASN C 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113120 restraints weight = 14517.978| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.06 r_work: 0.3208 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10665 Z= 0.119 Angle : 0.520 6.465 14463 Z= 0.269 Chirality : 0.042 0.369 1743 Planarity : 0.003 0.022 1812 Dihedral : 4.077 17.898 1428 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.50 % Allowed : 28.96 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1344 helix: 1.45 (0.27), residues: 414 sheet: 0.38 (0.29), residues: 324 loop : -1.11 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.002 0.001 HIS C 317 PHE 0.028 0.001 PHE A 351 TYR 0.013 0.001 TYR B 417 ARG 0.001 0.000 ARG C 282 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 411) hydrogen bonds : angle 4.82492 ( 1125) SS BOND : bond 0.00387 ( 21) SS BOND : angle 1.15779 ( 42) covalent geometry : bond 0.00275 (10644) covalent geometry : angle 0.51664 (14421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 381 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8648 (m) cc_final: 0.8303 (p) REVERT: A 85 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8218 (mtpp) REVERT: A 152 VAL cc_start: 0.8726 (m) cc_final: 0.8353 (t) REVERT: A 163 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6173 (mm-30) REVERT: A 226 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7941 (mmmm) REVERT: A 232 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: A 289 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7877 (tmm) REVERT: A 344 ASP cc_start: 0.7623 (t0) cc_final: 0.7361 (t0) REVERT: A 351 PHE cc_start: 0.8584 (t80) cc_final: 0.8336 (t80) REVERT: A 393 CYS cc_start: 0.7493 (m) cc_final: 0.7254 (m) REVERT: A 433 LYS cc_start: 0.8464 (tttm) cc_final: 0.8169 (tttm) REVERT: A 454 ASN cc_start: 0.7989 (m-40) cc_final: 0.7773 (m110) REVERT: B 160 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7279 (mm) REVERT: B 236 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 238 SER cc_start: 0.8550 (t) cc_final: 0.8193 (p) REVERT: B 289 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7795 (tmm) REVERT: B 296 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7948 (m) REVERT: B 361 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: C 34 GLN cc_start: 0.8759 (tt0) cc_final: 0.8470 (tt0) REVERT: C 201 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7359 (mtmt) REVERT: C 222 GLU cc_start: 0.7908 (tp30) cc_final: 0.7323 (tp30) REVERT: C 226 LYS cc_start: 0.8266 (mmmm) cc_final: 0.8054 (mmmm) REVERT: C 236 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 289 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7729 (tmm) REVERT: C 338 ASP cc_start: 0.7075 (p0) cc_final: 0.6623 (p0) REVERT: C 343 CYS cc_start: 0.7485 (m) cc_final: 0.7282 (m) REVERT: C 351 PHE cc_start: 0.8470 (t80) cc_final: 0.8123 (t80) REVERT: C 361 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: C 393 CYS cc_start: 0.7588 (m) cc_final: 0.7331 (m) REVERT: C 399 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7539 (pttm) outliers start: 68 outliers final: 56 residues processed: 410 average time/residue: 0.2270 time to fit residues: 129.6706 Evaluate side-chains 440 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 375 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Chi-restraints excluded: chain C residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 270 GLN B 454 ASN C 225 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.111756 restraints weight = 14373.423| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.05 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10665 Z= 0.156 Angle : 0.551 6.718 14463 Z= 0.286 Chirality : 0.042 0.363 1743 Planarity : 0.003 0.023 1812 Dihedral : 4.152 18.104 1428 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.42 % Allowed : 29.05 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.23), residues: 1344 helix: 1.20 (0.26), residues: 432 sheet: 0.33 (0.29), residues: 324 loop : -1.11 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.028 0.001 PHE A 351 TYR 0.017 0.001 TYR B 417 ARG 0.002 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 411) hydrogen bonds : angle 4.84837 ( 1125) SS BOND : bond 0.00403 ( 21) SS BOND : angle 1.43963 ( 42) covalent geometry : bond 0.00359 (10644) covalent geometry : angle 0.54634 (14421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 381 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8688 (m) cc_final: 0.8401 (p) REVERT: A 85 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8246 (mtpp) REVERT: A 152 VAL cc_start: 0.8754 (m) cc_final: 0.8390 (t) REVERT: A 163 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6231 (mm-30) REVERT: A 226 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8018 (mmmm) REVERT: A 232 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 289 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7884 (tmm) REVERT: A 344 ASP cc_start: 0.7654 (t0) cc_final: 0.7377 (t0) REVERT: A 351 PHE cc_start: 0.8594 (t80) cc_final: 0.8337 (t80) REVERT: A 393 CYS cc_start: 0.7511 (m) cc_final: 0.7272 (m) REVERT: A 428 ASN cc_start: 0.8376 (t0) cc_final: 0.8127 (t0) REVERT: A 433 LYS cc_start: 0.8485 (tttm) cc_final: 0.8208 (tttm) REVERT: A 454 ASN cc_start: 0.7944 (m110) cc_final: 0.7728 (m110) REVERT: B 78 LEU cc_start: 0.8482 (mt) cc_final: 0.8170 (mp) REVERT: B 160 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7283 (mm) REVERT: B 236 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 238 SER cc_start: 0.8556 (t) cc_final: 0.8181 (p) REVERT: B 272 LYS cc_start: 0.7859 (mtpp) cc_final: 0.7507 (ttpp) REVERT: B 289 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7814 (tmm) REVERT: B 296 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (m) REVERT: B 349 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8107 (m) REVERT: B 361 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: C 34 GLN cc_start: 0.8790 (tt0) cc_final: 0.8515 (tt0) REVERT: C 201 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7371 (mtmt) REVERT: C 222 GLU cc_start: 0.7906 (tp30) cc_final: 0.7344 (tp30) REVERT: C 226 LYS cc_start: 0.8308 (mmmm) cc_final: 0.8074 (mmmm) REVERT: C 236 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 289 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7733 (tmm) REVERT: C 338 ASP cc_start: 0.7085 (p0) cc_final: 0.6660 (p0) REVERT: C 343 CYS cc_start: 0.7503 (m) cc_final: 0.7274 (m) REVERT: C 351 PHE cc_start: 0.8488 (t80) cc_final: 0.8151 (t80) REVERT: C 361 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6818 (tm-30) REVERT: C 393 CYS cc_start: 0.7617 (m) cc_final: 0.7362 (m) REVERT: C 399 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7581 (pttm) outliers start: 67 outliers final: 53 residues processed: 408 average time/residue: 0.2181 time to fit residues: 123.8903 Evaluate side-chains 440 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 377 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 72 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 283 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113984 restraints weight = 14325.520| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.05 r_work: 0.3238 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10665 Z= 0.116 Angle : 0.525 6.630 14463 Z= 0.272 Chirality : 0.042 0.420 1743 Planarity : 0.003 0.022 1812 Dihedral : 4.029 18.410 1428 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.10 % Allowed : 29.21 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1344 helix: 1.25 (0.26), residues: 432 sheet: 0.28 (0.29), residues: 327 loop : -1.06 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.001 0.000 HIS A 317 PHE 0.026 0.001 PHE A 351 TYR 0.017 0.001 TYR B 417 ARG 0.001 0.000 ARG C 282 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 411) hydrogen bonds : angle 4.77205 ( 1125) SS BOND : bond 0.00381 ( 21) SS BOND : angle 1.43624 ( 42) covalent geometry : bond 0.00266 (10644) covalent geometry : angle 0.52011 (14421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.22 seconds wall clock time: 107 minutes 1.32 seconds (6421.32 seconds total)