Starting phenix.real_space_refine on Fri Jan 17 05:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ye3_39188/01_2025/8ye3_39188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ye3_39188/01_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_39188/01_2025/8ye3_39188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ye3_39188/01_2025/8ye3_39188.map" model { file = "/net/cci-nas-00/data/ceres_data/8ye3_39188/01_2025/8ye3_39188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ye3_39188/01_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-5571/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: 6.43, per 1000 atoms: 0.61 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=7, 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 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: 2.67 Conformation dependent library (CDL) restraints added in 1.3 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: 1.24 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: 3.42 Time building geometry restraints manager: 3.07 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: 5520 17.66 - 35.33: 728 35.33 - 52.99: 238 52.99 - 70.66: 38 70.66 - 88.32: 13 Dihedral angle restraints: 6537 sinusoidal: 2556 harmonic: 3981 Sorted by residual: 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 A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual -86.00 -137.92 51.92 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 343 " pdb=" CB CYS A 343 " ideal model delta sinusoidal sigma weight residual -86.00 -121.29 35.29 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 6534 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: 2.03 - 2.60: 125 2.60 - 3.18: 8795 3.18 - 3.75: 15930 3.75 - 4.33: 21570 4.33 - 4.90: 36421 Nonbonded interactions: 82841 Sorted by model distance: nonbonded pdb=" SG CYS B 313 " pdb=" SG CYS B 343 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 313 " pdb=" SG CYS C 343 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 322 " pdb=" SG CYS B 333 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 322 " pdb=" SG CYS C 333 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " model vdw 2.030 3.760 ... (remaining 82836 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: 0.07 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: 1.340 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.590 Find NCS groups from input model: 0.200 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- 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 10644 Z= 0.218 Angle : 0.534 10.396 14421 Z= 0.284 Chirality : 0.042 0.289 1743 Planarity : 0.005 0.087 1812 Dihedral : 17.687 88.319 3936 Min Nonbonded Distance : 2.028 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 *********************** 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 : 1.116 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: 0.2111 time to fit residues: 106.1476 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 : 1.099 ------------------------------------------------------------------------------- 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: 6.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3484 r_free = 0.3484 target = 0.121987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108028 restraints weight = 15000.387| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.11 r_work: 0.3160 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10644 Z= 0.378 Angle : 0.634 8.664 14421 Z= 0.329 Chirality : 0.045 0.232 1743 Planarity : 0.004 0.027 1812 Dihedral : 5.673 56.805 1454 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.50 % Allowed : 27.10 % Favored : 67.39 % 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: -0.18 (0.23), residues: 1344 helix: 0.81 (0.26), residues: 432 sheet: 0.35 (0.28), residues: 357 loop : -1.14 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 314 HIS 0.006 0.002 HIS C 317 PHE 0.017 0.002 PHE C 32 TYR 0.017 0.002 TYR A 342 ARG 0.004 0.001 ARG B 229 *********************** 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 450 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 382 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8008 (tp30) cc_final: 0.7798 (tp30) REVERT: A 146 SER cc_start: 0.8285 (t) cc_final: 0.8003 (t) REVERT: A 152 VAL cc_start: 0.8785 (m) cc_final: 0.8442 (t) REVERT: A 218 GLU cc_start: 0.8021 (mp0) cc_final: 0.7604 (mp0) REVERT: A 236 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 289 MET cc_start: 0.8189 (mmm) cc_final: 0.7881 (tmm) REVERT: A 318 THR cc_start: 0.8646 (m) cc_final: 0.8444 (p) REVERT: A 378 GLU cc_start: 0.8183 (mp0) cc_final: 0.7968 (mp0) REVERT: A 444 ASN cc_start: 0.7872 (p0) cc_final: 0.7490 (p0) REVERT: B 82 GLU cc_start: 0.8005 (tp30) cc_final: 0.7804 (tp30) REVERT: B 160 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7436 (mm) REVERT: B 163 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6222 (mm-30) REVERT: B 174 THR cc_start: 0.8046 (t) cc_final: 0.7763 (p) REVERT: B 218 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: B 232 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: B 236 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 238 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 289 MET cc_start: 0.8298 (mmm) cc_final: 0.8030 (tpp) REVERT: B 333 CYS cc_start: 0.7792 (t) cc_final: 0.7436 (m) REVERT: B 343 CYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7643 (m) REVERT: B 399 LYS cc_start: 0.8154 (pttm) cc_final: 0.7818 (pttm) REVERT: B 421 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8110 (mmpt) REVERT: B 428 ASN cc_start: 0.8499 (t0) cc_final: 0.8273 (t0) REVERT: B 444 ASN cc_start: 0.8120 (p0) cc_final: 0.7908 (p0) REVERT: B 478 TYR cc_start: 0.7975 (m-10) cc_final: 0.7670 (m-10) REVERT: C 34 GLN cc_start: 0.8763 (tt0) cc_final: 0.8508 (tt0) REVERT: C 37 CYS cc_start: 0.8800 (t) cc_final: 0.7984 (t) REVERT: C 38 SER cc_start: 0.8565 (p) cc_final: 0.8361 (m) REVERT: C 82 GLU cc_start: 0.7898 (tp30) cc_final: 0.7696 (tp30) REVERT: C 84 ASP cc_start: 0.7725 (t0) cc_final: 0.7503 (t0) REVERT: C 171 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 222 GLU cc_start: 0.7997 (tp30) cc_final: 0.7539 (tp30) REVERT: C 289 MET cc_start: 0.8245 (mmm) cc_final: 0.7856 (tmm) REVERT: C 333 CYS cc_start: 0.7771 (t) cc_final: 0.7555 (m) REVERT: C 338 ASP cc_start: 0.7187 (p0) cc_final: 0.6851 (p0) REVERT: C 343 CYS cc_start: 0.7998 (m) cc_final: 0.7296 (m) REVERT: C 351 PHE cc_start: 0.8455 (t80) cc_final: 0.8199 (t80) REVERT: C 422 CYS cc_start: 0.8465 (m) cc_final: 0.8098 (m) REVERT: C 478 TYR cc_start: 0.7995 (m-10) cc_final: 0.7759 (m-10) outliers start: 68 outliers final: 23 residues processed: 405 average time/residue: 0.2136 time to fit residues: 122.9990 Evaluate side-chains 397 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 367 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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 218 GLU 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 343 CYS 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 513 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 196 LYS 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 357 THR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 270 GLN 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 = 0.3538 r_free = 0.3538 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112716 restraints weight = 14725.479| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.02 r_work: 0.3170 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10644 Z= 0.205 Angle : 0.535 7.260 14421 Z= 0.277 Chirality : 0.042 0.231 1743 Planarity : 0.003 0.025 1812 Dihedral : 4.246 25.907 1429 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.10 % Allowed : 28.24 % Favored : 66.67 % 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: 1.21 (0.27), residues: 414 sheet: 0.40 (0.29), residues: 327 loop : -1.18 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.002 0.001 HIS C 317 PHE 0.023 0.001 PHE A 32 TYR 0.016 0.001 TYR B 417 ARG 0.002 0.000 ARG B 282 *********************** 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 434 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 371 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.7469 (mt) cc_final: 0.7264 (mt) REVERT: A 82 GLU cc_start: 0.7949 (tp30) cc_final: 0.7664 (tp30) REVERT: A 152 VAL cc_start: 0.8745 (m) cc_final: 0.8376 (t) REVERT: A 218 GLU cc_start: 0.7909 (mp0) cc_final: 0.7563 (mp0) REVERT: A 232 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 236 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7444 (mt-10) REVERT: A 289 MET cc_start: 0.8174 (mmm) cc_final: 0.7925 (tmm) REVERT: A 318 THR cc_start: 0.8574 (m) cc_final: 0.8342 (p) REVERT: A 454 ASN cc_start: 0.8044 (m-40) cc_final: 0.7819 (m-40) REVERT: B 82 GLU cc_start: 0.7906 (tp30) cc_final: 0.7668 (tp30) REVERT: B 160 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (mm) REVERT: B 163 GLU cc_start: 0.6533 (mm-30) cc_final: 0.6189 (mm-30) REVERT: B 174 THR cc_start: 0.8036 (t) cc_final: 0.7782 (p) REVERT: B 222 GLU cc_start: 0.7926 (tp30) cc_final: 0.7623 (tp30) REVERT: B 236 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 238 SER cc_start: 0.8628 (t) cc_final: 0.8259 (p) REVERT: B 333 CYS cc_start: 0.7548 (t) cc_final: 0.7296 (m) REVERT: B 378 GLU cc_start: 0.8093 (mp0) cc_final: 0.7886 (mp0) REVERT: B 399 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7774 (pttm) REVERT: B 428 ASN cc_start: 0.8418 (t0) cc_final: 0.8143 (t0) REVERT: B 478 TYR cc_start: 0.7888 (m-10) cc_final: 0.7584 (m-10) REVERT: C 34 GLN cc_start: 0.8790 (tt0) cc_final: 0.8435 (tt0) REVERT: C 222 GLU cc_start: 0.7928 (tp30) cc_final: 0.7333 (tp30) REVERT: C 225 GLN cc_start: 0.8114 (mt0) cc_final: 0.7803 (mt0) REVERT: C 236 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7537 (mt-10) REVERT: C 251 MET cc_start: 0.8049 (mtt) cc_final: 0.7796 (mtp) REVERT: C 333 CYS cc_start: 0.7529 (t) cc_final: 0.7309 (m) REVERT: C 338 ASP cc_start: 0.7108 (p0) cc_final: 0.6733 (p0) REVERT: C 399 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7786 (pttm) REVERT: C 422 CYS cc_start: 0.8510 (m) cc_final: 0.8274 (m) REVERT: C 513 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7588 (mt) outliers start: 63 outliers final: 39 residues processed: 394 average time/residue: 0.2273 time to fit residues: 127.5056 Evaluate side-chains 405 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 319 SER 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 A residue 513 LEU 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 319 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 447 VAL 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 167 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 357 THR 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 419 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 Chi-restraints excluded: chain C residue 513 LEU 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: 2.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN B 34 GLN B 270 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109700 restraints weight = 14566.757| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.00 r_work: 0.3156 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10644 Z= 0.348 Angle : 0.604 8.005 14421 Z= 0.312 Chirality : 0.045 0.319 1743 Planarity : 0.003 0.037 1812 Dihedral : 4.491 18.238 1428 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.80 % Allowed : 27.18 % Favored : 66.02 % 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: -0.18 (0.23), residues: 1344 helix: 1.15 (0.26), residues: 414 sheet: 0.21 (0.29), residues: 327 loop : -1.22 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 314 HIS 0.005 0.002 HIS B 317 PHE 0.030 0.002 PHE C 509 TYR 0.014 0.002 TYR B 417 ARG 0.003 0.000 ARG B 282 *********************** 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 470 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 386 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7887 (tp30) cc_final: 0.7652 (tp30) REVERT: A 152 VAL cc_start: 0.8807 (m) cc_final: 0.8434 (t) REVERT: A 163 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 218 GLU cc_start: 0.7972 (mp0) cc_final: 0.7545 (mp0) REVERT: A 222 GLU cc_start: 0.7831 (tp30) cc_final: 0.7366 (tp30) REVERT: A 232 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 236 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7502 (mt-10) REVERT: A 289 MET cc_start: 0.8252 (tmm) cc_final: 0.7975 (tpp) REVERT: A 454 ASN cc_start: 0.7988 (m-40) cc_final: 0.7724 (m-40) REVERT: A 461 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8174 (mmtt) REVERT: B 78 LEU cc_start: 0.8404 (mt) cc_final: 0.8102 (mp) REVERT: B 82 GLU cc_start: 0.7858 (tp30) cc_final: 0.7651 (tp30) REVERT: B 160 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7351 (mm) REVERT: B 163 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6287 (mm-30) REVERT: B 174 THR cc_start: 0.8124 (t) cc_final: 0.7921 (p) REVERT: B 176 LYS cc_start: 0.7957 (mttt) cc_final: 0.7755 (mttt) REVERT: B 236 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 238 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 296 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7984 (m) REVERT: B 333 CYS cc_start: 0.7453 (t) cc_final: 0.7241 (m) REVERT: B 428 ASN cc_start: 0.8454 (t0) cc_final: 0.8214 (t0) REVERT: B 478 TYR cc_start: 0.8001 (m-10) cc_final: 0.7782 (m-10) REVERT: C 34 GLN cc_start: 0.8868 (tt0) cc_final: 0.8596 (tt0) REVERT: C 163 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6441 (mm-30) REVERT: C 171 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 174 THR cc_start: 0.8397 (t) cc_final: 0.8104 (p) REVERT: C 222 GLU cc_start: 0.8012 (tp30) cc_final: 0.7581 (tp30) REVERT: C 225 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: C 236 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 289 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7754 (tmm) REVERT: C 338 ASP cc_start: 0.7077 (p0) cc_final: 0.6781 (p0) REVERT: C 361 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: C 399 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7778 (pttm) REVERT: C 416 CYS cc_start: 0.8484 (p) cc_final: 0.8137 (p) REVERT: C 422 CYS cc_start: 0.8591 (m) cc_final: 0.8385 (m) outliers start: 84 outliers final: 47 residues processed: 413 average time/residue: 0.2249 time to fit residues: 129.9495 Evaluate side-chains 424 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 368 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 168 LYS 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 368 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 432 ILE 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 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 296 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL 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 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 171 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 225 GLN 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 253 THR Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 368 ASP 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 419 LYS Chi-restraints excluded: chain C residue 440 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111770 restraints weight = 14525.577| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.03 r_work: 0.3193 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10644 Z= 0.214 Angle : 0.544 7.116 14421 Z= 0.281 Chirality : 0.042 0.297 1743 Planarity : 0.003 0.034 1812 Dihedral : 4.321 18.844 1428 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.39 % Allowed : 27.99 % Favored : 65.61 % 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: 1.29 (0.27), residues: 414 sheet: 0.14 (0.29), residues: 327 loop : -1.15 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.027 0.001 PHE A 32 TYR 0.024 0.001 TYR C 417 ARG 0.002 0.000 ARG B 282 *********************** 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 447 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 368 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 VAL cc_start: 0.8416 (m) cc_final: 0.8149 (t) REVERT: A 82 GLU cc_start: 0.7903 (tp30) cc_final: 0.7621 (tp30) REVERT: A 152 VAL cc_start: 0.8754 (m) cc_final: 0.8386 (t) REVERT: A 163 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6254 (mm-30) REVERT: A 218 GLU cc_start: 0.7980 (mp0) cc_final: 0.7651 (mp0) REVERT: A 222 GLU cc_start: 0.7758 (tp30) cc_final: 0.7241 (tp30) REVERT: A 232 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 236 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 289 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (tpp) REVERT: A 454 ASN cc_start: 0.8029 (m-40) cc_final: 0.7713 (m110) REVERT: A 461 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8161 (mmtt) REVERT: B 82 GLU cc_start: 0.7922 (tp30) cc_final: 0.7713 (tp30) REVERT: B 160 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7322 (mm) REVERT: B 236 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7482 (mt-10) REVERT: B 238 SER cc_start: 0.8584 (t) cc_final: 0.8235 (p) REVERT: B 289 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7707 (tmm) REVERT: B 296 VAL cc_start: 0.8272 (OUTLIER) cc_final: 0.7947 (m) REVERT: B 361 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: B 399 LYS cc_start: 0.8322 (pttm) cc_final: 0.7813 (pttm) REVERT: B 428 ASN cc_start: 0.8418 (t0) cc_final: 0.8175 (t0) REVERT: C 34 GLN cc_start: 0.8793 (tt0) cc_final: 0.8489 (tt0) REVERT: C 42 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7437 (mtmm) REVERT: C 163 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6387 (mm-30) REVERT: C 174 THR cc_start: 0.8384 (t) cc_final: 0.8112 (p) REVERT: C 222 GLU cc_start: 0.7982 (tp30) cc_final: 0.7456 (tp30) REVERT: C 225 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: C 236 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7418 (mt-10) REVERT: C 289 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7709 (tmm) REVERT: C 327 LYS cc_start: 0.7690 (tppt) cc_final: 0.7487 (mppt) REVERT: C 338 ASP cc_start: 0.7138 (p0) cc_final: 0.6752 (p0) REVERT: C 361 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: C 399 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: C 416 CYS cc_start: 0.8292 (p) cc_final: 0.8055 (p) REVERT: C 422 CYS cc_start: 0.8546 (m) cc_final: 0.8336 (m) REVERT: C 454 ASN cc_start: 0.7909 (m-40) cc_final: 0.7657 (m-40) REVERT: C 494 GLN cc_start: 0.8226 (mt0) cc_final: 0.7818 (mt0) outliers start: 79 outliers final: 49 residues processed: 398 average time/residue: 0.2127 time to fit residues: 119.9671 Evaluate side-chains 417 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 368 ASP Chi-restraints excluded: chain A residue 396 MET 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 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 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL 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 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 36 THR 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 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 368 ASP 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 419 LYS Chi-restraints excluded: chain C residue 425 SER 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 509 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 48 optimal weight: 0.0670 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 454 ASN B 270 GLN B 345 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** 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 = 0.3515 r_free = 0.3515 target = 0.124149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110230 restraints weight = 14665.996| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.05 r_work: 0.3164 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10644 Z= 0.236 Angle : 0.552 9.250 14421 Z= 0.284 Chirality : 0.043 0.327 1743 Planarity : 0.003 0.033 1812 Dihedral : 4.326 19.627 1428 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.39 % Allowed : 28.56 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1344 helix: 1.30 (0.27), residues: 414 sheet: 0.14 (0.29), residues: 327 loop : -1.14 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.028 0.001 PHE A 32 TYR 0.029 0.001 TYR B 417 ARG 0.002 0.000 ARG B 282 *********************** 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 436 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 357 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8631 (m) cc_final: 0.8341 (p) REVERT: A 40 VAL cc_start: 0.8423 (m) cc_final: 0.8161 (t) REVERT: A 82 GLU cc_start: 0.7933 (tp30) cc_final: 0.7637 (tp30) REVERT: A 152 VAL cc_start: 0.8764 (m) cc_final: 0.8387 (t) REVERT: A 163 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6260 (mm-30) REVERT: A 218 GLU cc_start: 0.7978 (mp0) cc_final: 0.7675 (mp0) REVERT: A 222 GLU cc_start: 0.7808 (tp30) cc_final: 0.7362 (tp30) REVERT: A 226 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8046 (mmmm) REVERT: A 232 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 289 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: A 344 ASP cc_start: 0.7808 (t0) cc_final: 0.7585 (t0) REVERT: A 378 GLU cc_start: 0.8253 (mp0) cc_final: 0.8010 (mp0) REVERT: A 454 ASN cc_start: 0.7975 (m110) cc_final: 0.7745 (m110) REVERT: A 461 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8145 (mmtt) REVERT: B 78 LEU cc_start: 0.8455 (mt) cc_final: 0.8141 (mp) REVERT: B 82 GLU cc_start: 0.7890 (tp30) cc_final: 0.7669 (tp30) REVERT: B 160 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7309 (mm) REVERT: B 236 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 238 SER cc_start: 0.8615 (t) cc_final: 0.8263 (p) REVERT: B 289 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7844 (tmm) REVERT: B 296 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.7987 (m) REVERT: B 352 PHE cc_start: 0.8351 (m-80) cc_final: 0.7884 (m-80) REVERT: B 361 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: B 399 LYS cc_start: 0.8270 (pttm) cc_final: 0.8032 (pttm) REVERT: B 428 ASN cc_start: 0.8397 (t0) cc_final: 0.8158 (t0) REVERT: C 34 GLN cc_start: 0.8837 (tt0) cc_final: 0.8555 (tt0) REVERT: C 163 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6416 (mm-30) REVERT: C 174 THR cc_start: 0.8299 (t) cc_final: 0.8060 (p) REVERT: C 222 GLU cc_start: 0.7985 (tp30) cc_final: 0.7497 (tp30) REVERT: C 225 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: C 236 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 289 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: C 338 ASP cc_start: 0.7098 (p0) cc_final: 0.6743 (p0) REVERT: C 361 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: C 399 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7800 (pttm) REVERT: C 416 CYS cc_start: 0.8461 (p) cc_final: 0.8230 (p) REVERT: C 417 TYR cc_start: 0.8125 (m-80) cc_final: 0.7876 (m-10) REVERT: C 422 CYS cc_start: 0.8564 (m) cc_final: 0.8363 (m) REVERT: C 454 ASN cc_start: 0.7878 (m-40) cc_final: 0.7624 (m-40) outliers start: 79 outliers final: 56 residues processed: 388 average time/residue: 0.2143 time to fit residues: 117.6148 Evaluate side-chains 416 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 350 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 189 THR 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 349 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 ASN 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 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 357 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 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 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 36 THR 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 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 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 419 LYS Chi-restraints excluded: chain C residue 425 SER 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 502 SER Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE 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: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110901 restraints weight = 14710.837| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.04 r_work: 0.3179 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10644 Z= 0.255 Angle : 0.559 7.974 14421 Z= 0.290 Chirality : 0.043 0.351 1743 Planarity : 0.003 0.034 1812 Dihedral : 4.381 20.475 1428 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.72 % Allowed : 28.24 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1344 helix: 1.26 (0.26), residues: 414 sheet: 0.11 (0.29), residues: 327 loop : -1.14 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.022 0.001 PHE A 351 TYR 0.028 0.001 TYR B 417 ARG 0.002 0.000 ARG A 229 *********************** 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 451 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 368 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8663 (m) cc_final: 0.8333 (p) REVERT: A 40 VAL cc_start: 0.8427 (m) cc_final: 0.8163 (t) REVERT: A 82 GLU cc_start: 0.7959 (tp30) cc_final: 0.7674 (tp30) REVERT: A 152 VAL cc_start: 0.8762 (m) cc_final: 0.8390 (t) REVERT: A 163 GLU cc_start: 0.6601 (mm-30) cc_final: 0.6281 (mm-30) REVERT: A 218 GLU cc_start: 0.7941 (mp0) cc_final: 0.7633 (mp0) REVERT: A 222 GLU cc_start: 0.7793 (tp30) cc_final: 0.7288 (tp30) REVERT: A 226 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8068 (mmmm) REVERT: A 232 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: A 289 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: A 344 ASP cc_start: 0.7819 (t0) cc_final: 0.7603 (t0) REVERT: A 378 GLU cc_start: 0.8237 (mp0) cc_final: 0.8018 (mp0) REVERT: A 393 CYS cc_start: 0.7570 (m) cc_final: 0.7340 (m) REVERT: A 454 ASN cc_start: 0.7954 (m110) cc_final: 0.7734 (m110) REVERT: A 461 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8160 (mmtt) REVERT: B 82 GLU cc_start: 0.7920 (tp30) cc_final: 0.7678 (tp30) REVERT: B 160 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7298 (mm) REVERT: B 236 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 238 SER cc_start: 0.8632 (t) cc_final: 0.8227 (p) REVERT: B 289 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7908 (tmm) REVERT: B 296 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7972 (m) REVERT: B 361 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: B 399 LYS cc_start: 0.8238 (pttm) cc_final: 0.7917 (pttm) REVERT: B 428 ASN cc_start: 0.8384 (t0) cc_final: 0.8149 (t0) REVERT: C 34 GLN cc_start: 0.8832 (tt0) cc_final: 0.8505 (tt0) REVERT: C 222 GLU cc_start: 0.7969 (tp30) cc_final: 0.7452 (tp30) REVERT: C 225 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: C 236 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7426 (mt-10) REVERT: C 289 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: C 338 ASP cc_start: 0.7109 (p0) cc_final: 0.6734 (p0) REVERT: C 361 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: C 399 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7763 (pttm) REVERT: C 417 TYR cc_start: 0.8084 (m-80) cc_final: 0.7871 (m-10) REVERT: C 422 CYS cc_start: 0.8550 (m) cc_final: 0.8339 (m) REVERT: C 454 ASN cc_start: 0.7881 (m-40) cc_final: 0.7658 (m110) outliers start: 83 outliers final: 62 residues processed: 399 average time/residue: 0.2194 time to fit residues: 123.7283 Evaluate side-chains 437 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 365 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 95 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 189 THR 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 264 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 ASN 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 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 344 ASP Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL Chi-restraints excluded: chain B residue 405 SER 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 508 LYS Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 36 THR 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 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 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 419 LYS Chi-restraints excluded: chain C residue 425 SER 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 509 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110673 restraints weight = 14601.861| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.04 r_work: 0.3168 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10644 Z= 0.221 Angle : 0.542 7.872 14421 Z= 0.280 Chirality : 0.043 0.367 1743 Planarity : 0.003 0.032 1812 Dihedral : 4.327 18.422 1428 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.88 % Allowed : 28.80 % Favored : 64.32 % 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: -0.20 (0.23), residues: 1344 helix: 1.03 (0.26), residues: 432 sheet: 0.17 (0.29), residues: 324 loop : -1.16 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.002 0.001 HIS A 317 PHE 0.026 0.001 PHE A 351 TYR 0.026 0.001 TYR B 417 ARG 0.002 0.000 ARG B 282 *********************** 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 450 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 365 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8651 (m) cc_final: 0.8275 (p) REVERT: A 40 VAL cc_start: 0.8421 (m) cc_final: 0.8160 (t) REVERT: A 82 GLU cc_start: 0.7918 (tp30) cc_final: 0.7590 (tp30) REVERT: A 152 VAL cc_start: 0.8736 (m) cc_final: 0.8366 (t) REVERT: A 163 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6266 (mm-30) REVERT: A 222 GLU cc_start: 0.7823 (tp30) cc_final: 0.7325 (tp30) REVERT: A 226 LYS cc_start: 0.8299 (mmmm) cc_final: 0.7998 (mmmm) REVERT: A 232 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 289 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7915 (tmm) REVERT: A 378 GLU cc_start: 0.8241 (mp0) cc_final: 0.8032 (mp0) REVERT: A 393 CYS cc_start: 0.7539 (m) cc_final: 0.7307 (m) REVERT: A 454 ASN cc_start: 0.7979 (m110) cc_final: 0.7765 (m110) REVERT: A 461 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8134 (mmtt) REVERT: B 82 GLU cc_start: 0.7858 (tp30) cc_final: 0.7627 (tp30) REVERT: B 160 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7289 (mm) REVERT: B 236 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 238 SER cc_start: 0.8572 (t) cc_final: 0.8220 (p) REVERT: B 289 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7919 (tmm) REVERT: B 296 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7959 (m) REVERT: B 361 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: B 428 ASN cc_start: 0.8368 (t0) cc_final: 0.8133 (t0) REVERT: C 34 GLN cc_start: 0.8823 (tt0) cc_final: 0.8503 (tt0) REVERT: C 201 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7426 (mtmt) REVERT: C 222 GLU cc_start: 0.7947 (tp30) cc_final: 0.7421 (tp30) REVERT: C 225 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: C 236 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 289 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: C 338 ASP cc_start: 0.7054 (p0) cc_final: 0.6668 (p0) REVERT: C 361 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: C 399 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: C 417 TYR cc_start: 0.8147 (m-80) cc_final: 0.7919 (m-10) REVERT: C 454 ASN cc_start: 0.7876 (m-40) cc_final: 0.7633 (m110) outliers start: 85 outliers final: 65 residues processed: 395 average time/residue: 0.2194 time to fit residues: 123.1034 Evaluate side-chains 435 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 189 THR 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 264 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN 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 501 GLN 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 319 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL Chi-restraints excluded: chain B residue 405 SER 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 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 165 ASN Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 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 419 LYS Chi-restraints excluded: chain C residue 425 SER 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 502 SER Chi-restraints excluded: chain C residue 503 LEU 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: 0.6980 chunk 106 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111484 restraints weight = 14768.024| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.04 r_work: 0.3206 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10644 Z= 0.187 Angle : 0.533 7.580 14421 Z= 0.277 Chirality : 0.043 0.408 1743 Planarity : 0.003 0.031 1812 Dihedral : 4.271 20.211 1428 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.15 % Allowed : 29.29 % Favored : 64.56 % 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: -0.14 (0.23), residues: 1344 helix: 1.09 (0.26), residues: 432 sheet: 0.22 (0.29), residues: 324 loop : -1.15 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.002 0.001 HIS A 317 PHE 0.014 0.001 PHE A 32 TYR 0.031 0.001 TYR B 417 ARG 0.002 0.000 ARG C 282 *********************** 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 438 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 362 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8695 (m) cc_final: 0.8302 (p) REVERT: A 40 VAL cc_start: 0.8322 (m) cc_final: 0.8057 (t) REVERT: A 82 GLU cc_start: 0.7944 (tp30) cc_final: 0.7597 (tp30) REVERT: A 152 VAL cc_start: 0.8704 (m) cc_final: 0.8336 (t) REVERT: A 163 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6226 (mm-30) REVERT: A 232 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: A 289 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: A 322 CYS cc_start: 0.6999 (m) cc_final: 0.6665 (m) REVERT: A 393 CYS cc_start: 0.7525 (m) cc_final: 0.7295 (m) REVERT: A 454 ASN cc_start: 0.8016 (m110) cc_final: 0.7794 (m110) REVERT: A 461 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8086 (mmtt) REVERT: B 82 GLU cc_start: 0.7892 (tp30) cc_final: 0.7678 (tp30) REVERT: B 160 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7312 (mm) REVERT: B 236 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7521 (mt-10) REVERT: B 238 SER cc_start: 0.8542 (t) cc_final: 0.8174 (p) REVERT: B 277 ASN cc_start: 0.8170 (m-40) cc_final: 0.7776 (m-40) REVERT: B 289 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: B 296 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7970 (m) REVERT: B 417 TYR cc_start: 0.7885 (m-10) cc_final: 0.7597 (m-10) REVERT: B 419 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7814 (mtmt) REVERT: B 428 ASN cc_start: 0.8366 (t0) cc_final: 0.8138 (t0) REVERT: C 34 GLN cc_start: 0.8758 (tt0) cc_final: 0.8484 (tt0) REVERT: C 222 GLU cc_start: 0.7942 (tp30) cc_final: 0.7358 (tp30) REVERT: C 225 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: C 236 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 289 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7698 (tmm) REVERT: C 322 CYS cc_start: 0.7775 (m) cc_final: 0.7413 (m) REVERT: C 338 ASP cc_start: 0.7049 (p0) cc_final: 0.6628 (p0) REVERT: C 361 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: C 399 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7759 (pttm) outliers start: 76 outliers final: 60 residues processed: 393 average time/residue: 0.2325 time to fit residues: 130.2591 Evaluate side-chains 437 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 368 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 189 THR 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 264 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN 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 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 319 SER Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 482 VAL 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 161 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 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 419 LYS Chi-restraints excluded: chain C residue 425 SER 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 502 SER 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 25 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.0040 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 270 GLN B 437 ASN B 454 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN C 437 ASN C 454 ASN C 494 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113065 restraints weight = 14591.213| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.04 r_work: 0.3212 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10644 Z= 0.181 Angle : 0.539 7.135 14421 Z= 0.281 Chirality : 0.043 0.449 1743 Planarity : 0.003 0.031 1812 Dihedral : 4.239 23.771 1428 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.66 % Allowed : 30.02 % Favored : 64.32 % 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: 0.32 (0.29), residues: 324 loop : -1.16 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.013 0.001 PHE A 32 TYR 0.031 0.001 TYR B 417 ARG 0.001 0.000 ARG C 49 ********************** 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 435 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 365 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8701 (m) cc_final: 0.8288 (p) REVERT: A 82 GLU cc_start: 0.7917 (tp30) cc_final: 0.7562 (tp30) REVERT: A 152 VAL cc_start: 0.8696 (m) cc_final: 0.8328 (t) REVERT: A 163 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6222 (mm-30) REVERT: A 232 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: A 393 CYS cc_start: 0.7495 (m) cc_final: 0.7273 (m) REVERT: A 428 ASN cc_start: 0.8407 (t0) cc_final: 0.8140 (t0) REVERT: A 454 ASN cc_start: 0.8018 (m110) cc_final: 0.7807 (m110) REVERT: A 461 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8148 (mmtt) REVERT: B 82 GLU cc_start: 0.7918 (tp30) cc_final: 0.7709 (tp30) REVERT: B 160 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7316 (mm) REVERT: B 236 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 238 SER cc_start: 0.8530 (t) cc_final: 0.8171 (p) REVERT: B 289 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7903 (tmm) REVERT: B 296 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.7941 (m) REVERT: B 419 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7797 (mtmt) REVERT: B 428 ASN cc_start: 0.8352 (t0) cc_final: 0.8121 (t0) REVERT: C 34 GLN cc_start: 0.8759 (tt0) cc_final: 0.8405 (tt0) REVERT: C 222 GLU cc_start: 0.7979 (tp30) cc_final: 0.7364 (tp30) REVERT: C 225 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: C 236 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 289 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7653 (tmm) REVERT: C 322 CYS cc_start: 0.7929 (m) cc_final: 0.7725 (m) REVERT: C 338 ASP cc_start: 0.7037 (p0) cc_final: 0.6626 (p0) REVERT: C 361 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: C 478 TYR cc_start: 0.7953 (m-10) cc_final: 0.7691 (m-10) outliers start: 70 outliers final: 58 residues processed: 393 average time/residue: 0.2077 time to fit residues: 115.8821 Evaluate side-chains 427 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 362 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 189 THR 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 264 MET Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 371 ASN 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 335 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 368 ASP 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 402 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 454 ASN 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 161 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 244 THR 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 357 THR Chi-restraints excluded: chain C residue 361 GLN Chi-restraints excluded: chain C residue 362 SER 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 425 SER 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 502 SER 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 75 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 270 GLN B 437 ASN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 494 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109449 restraints weight = 14351.764| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.00 r_work: 0.3185 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10644 Z= 0.334 Angle : 0.617 7.738 14421 Z= 0.320 Chirality : 0.046 0.477 1743 Planarity : 0.003 0.034 1812 Dihedral : 4.606 23.576 1428 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.42 % Allowed : 30.91 % Favored : 63.67 % 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: -0.25 (0.22), residues: 1344 helix: 0.98 (0.26), residues: 432 sheet: 0.19 (0.29), residues: 324 loop : -1.23 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 314 HIS 0.004 0.001 HIS A 317 PHE 0.013 0.001 PHE A 32 TYR 0.055 0.002 TYR B 417 ARG 0.002 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4905.27 seconds wall clock time: 88 minutes 27.22 seconds (5307.22 seconds total)