Starting phenix.real_space_refine on Fri Oct 11 17:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_39188.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_39188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_39188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_39188.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ye3_39188/10_2024/8ye3_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 6.64, per 1000 atoms: 0.63 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: 3.01 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: 3.05 Time building geometry restraints manager: 3.17 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.250 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.900 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 11 poor density : 352 time to evaluate : 1.287 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: 0.2223 time to fit residues: 110.9911 Evaluate side-chains 342 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 332 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 fitting. rotamer outliers: 68 poor density : 382 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7710 (tp30) cc_final: 0.7433 (tp30) REVERT: A 146 SER cc_start: 0.7995 (t) cc_final: 0.7639 (t) REVERT: A 218 GLU cc_start: 0.7884 (mp0) cc_final: 0.7403 (mp0) REVERT: A 236 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6949 (mt-10) REVERT: A 289 MET cc_start: 0.8284 (mmm) cc_final: 0.8044 (tmm) REVERT: A 318 THR cc_start: 0.8445 (m) cc_final: 0.8117 (p) REVERT: A 378 GLU cc_start: 0.7747 (mp0) cc_final: 0.7407 (mp0) REVERT: A 444 ASN cc_start: 0.7736 (p0) cc_final: 0.7304 (p0) REVERT: A 448 ASP cc_start: 0.7829 (t0) cc_final: 0.7613 (t0) REVERT: B 30 GLU cc_start: 0.7591 (tt0) cc_final: 0.7329 (tt0) REVERT: B 38 SER cc_start: 0.8042 (p) cc_final: 0.7819 (m) REVERT: B 82 GLU cc_start: 0.7709 (tp30) cc_final: 0.7446 (tp30) REVERT: B 160 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6645 (mm) REVERT: B 163 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6536 (mm-30) REVERT: B 174 THR cc_start: 0.7797 (t) cc_final: 0.7484 (p) REVERT: B 218 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: B 232 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 236 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6947 (mt-10) REVERT: B 238 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7294 (p) REVERT: B 289 MET cc_start: 0.8309 (mmm) cc_final: 0.7986 (tpp) REVERT: B 313 CYS cc_start: 0.8249 (t) cc_final: 0.8032 (m) REVERT: B 333 CYS cc_start: 0.7552 (t) cc_final: 0.7144 (m) REVERT: B 343 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7821 (m) REVERT: B 399 LYS cc_start: 0.7909 (pttm) cc_final: 0.7542 (pttm) REVERT: B 405 SER cc_start: 0.8513 (p) cc_final: 0.8312 (p) REVERT: B 421 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7790 (mmpt) REVERT: B 428 ASN cc_start: 0.8425 (t0) cc_final: 0.8214 (t0) REVERT: B 444 ASN cc_start: 0.7908 (p0) cc_final: 0.7662 (p0) REVERT: B 488 PHE cc_start: 0.7956 (t80) cc_final: 0.7729 (t80) REVERT: C 37 CYS cc_start: 0.8525 (t) cc_final: 0.8255 (t) REVERT: C 38 SER cc_start: 0.7981 (p) cc_final: 0.7722 (m) REVERT: C 82 GLU cc_start: 0.7619 (tp30) cc_final: 0.7341 (tp30) REVERT: C 171 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (mp) REVERT: C 222 GLU cc_start: 0.8095 (tp30) cc_final: 0.7591 (tp30) REVERT: C 289 MET cc_start: 0.8200 (mmm) cc_final: 0.7949 (tmm) REVERT: C 333 CYS cc_start: 0.7545 (t) cc_final: 0.7308 (m) REVERT: C 338 ASP cc_start: 0.7052 (p0) cc_final: 0.6612 (p0) REVERT: C 351 PHE cc_start: 0.8242 (t80) cc_final: 0.7937 (t80) REVERT: C 422 CYS cc_start: 0.8684 (m) cc_final: 0.8176 (m) REVERT: C 478 TYR cc_start: 0.7508 (m-10) cc_final: 0.7303 (m-10) outliers start: 68 outliers final: 23 residues processed: 405 average time/residue: 0.2276 time to fit residues: 131.4578 Evaluate side-chains 399 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 369 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 68 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 34 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2274 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= 0.193 Angle : 0.526 7.171 14421 Z= 0.273 Chirality : 0.042 0.235 1743 Planarity : 0.003 0.025 1812 Dihedral : 4.218 25.836 1429 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.66 % Allowed : 27.91 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1344 helix: 1.22 (0.26), residues: 414 sheet: 0.42 (0.29), residues: 327 loop : -1.16 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.002 0.001 HIS C 317 PHE 0.022 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 442 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 372 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.7287 (mt) cc_final: 0.7055 (mt) REVERT: A 82 GLU cc_start: 0.7679 (tp30) cc_final: 0.7296 (tp30) REVERT: A 218 GLU cc_start: 0.7855 (mp0) cc_final: 0.7408 (mp0) REVERT: A 232 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 236 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6831 (mt-10) REVERT: A 289 MET cc_start: 0.8239 (mmm) cc_final: 0.8038 (tmm) REVERT: A 318 THR cc_start: 0.8434 (m) cc_final: 0.8025 (p) REVERT: A 370 MET cc_start: 0.8398 (ttm) cc_final: 0.8163 (ttm) REVERT: B 30 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7166 (tt0) REVERT: B 82 GLU cc_start: 0.7729 (tp30) cc_final: 0.7407 (tp30) REVERT: B 160 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6687 (mm) REVERT: B 163 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6450 (mm-30) REVERT: B 174 THR cc_start: 0.7803 (t) cc_final: 0.7502 (p) REVERT: B 222 GLU cc_start: 0.8048 (tp30) cc_final: 0.7740 (tp30) REVERT: B 236 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6878 (mt-10) REVERT: B 238 SER cc_start: 0.7968 (t) cc_final: 0.7409 (p) REVERT: B 289 MET cc_start: 0.8241 (tmm) cc_final: 0.7955 (tpp) REVERT: B 313 CYS cc_start: 0.8245 (t) cc_final: 0.8007 (m) REVERT: B 333 CYS cc_start: 0.7486 (t) cc_final: 0.7025 (m) REVERT: B 343 CYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7743 (m) REVERT: B 378 GLU cc_start: 0.7620 (mp0) cc_final: 0.7314 (mp0) REVERT: B 399 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7398 (pttm) REVERT: B 421 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7786 (mmpt) REVERT: B 428 ASN cc_start: 0.8408 (t0) cc_final: 0.8168 (t0) REVERT: B 488 PHE cc_start: 0.7930 (t80) cc_final: 0.7729 (t80) REVERT: C 82 GLU cc_start: 0.7594 (tp30) cc_final: 0.7284 (tp30) REVERT: C 218 GLU cc_start: 0.7801 (mp0) cc_final: 0.7550 (mp0) REVERT: C 222 GLU cc_start: 0.8066 (tp30) cc_final: 0.7419 (tp30) REVERT: C 225 GLN cc_start: 0.7977 (mt0) cc_final: 0.7708 (mt0) REVERT: C 236 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6930 (mt-10) REVERT: C 289 MET cc_start: 0.8156 (mmm) cc_final: 0.7934 (tmm) REVERT: C 319 SER cc_start: 0.8538 (t) cc_final: 0.8186 (p) REVERT: C 333 CYS cc_start: 0.7423 (t) cc_final: 0.7091 (m) REVERT: C 338 ASP cc_start: 0.7066 (p0) cc_final: 0.6561 (p0) REVERT: C 361 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6401 (tt0) REVERT: C 373 LEU cc_start: 0.8202 (mt) cc_final: 0.7967 (mp) REVERT: C 399 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7476 (pttm) REVERT: C 422 CYS cc_start: 0.8759 (m) cc_final: 0.8405 (m) outliers start: 70 outliers final: 40 residues processed: 395 average time/residue: 0.2369 time to fit residues: 133.0640 Evaluate side-chains 418 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 370 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 232 GLU 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 30 GLU Chi-restraints excluded: chain B residue 36 THR 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 343 CYS 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 421 LYS Chi-restraints excluded: chain B residue 447 VAL 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 361 GLN Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 419 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 0.0970 chunk 35 optimal weight: 0.0050 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10644 Z= 0.151 Angle : 0.487 6.738 14421 Z= 0.254 Chirality : 0.041 0.231 1743 Planarity : 0.003 0.029 1812 Dihedral : 3.936 17.545 1428 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.26 % Allowed : 28.64 % Favored : 66.10 % 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: 1.41 (0.27), residues: 414 sheet: 0.45 (0.30), residues: 324 loop : -1.09 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 314 HIS 0.002 0.001 HIS C 317 PHE 0.026 0.001 PHE A 32 TYR 0.013 0.001 TYR B 417 ARG 0.001 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 436 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 371 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: A 64 ILE cc_start: 0.7247 (mt) cc_final: 0.7015 (mt) REVERT: A 82 GLU cc_start: 0.7666 (tp30) cc_final: 0.7198 (tp30) REVERT: A 232 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: A 318 THR cc_start: 0.8414 (m) cc_final: 0.7965 (p) REVERT: A 461 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8073 (mmtt) REVERT: B 82 GLU cc_start: 0.7677 (tp30) cc_final: 0.7357 (tp30) REVERT: B 160 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6674 (mm) REVERT: B 163 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6423 (mm-30) REVERT: B 174 THR cc_start: 0.7789 (t) cc_final: 0.7486 (p) REVERT: B 222 GLU cc_start: 0.8025 (tp30) cc_final: 0.7696 (tp30) REVERT: B 236 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6870 (mt-10) REVERT: B 238 SER cc_start: 0.7903 (t) cc_final: 0.7365 (p) REVERT: B 289 MET cc_start: 0.8192 (tmm) cc_final: 0.7909 (tpp) REVERT: B 313 CYS cc_start: 0.8229 (t) cc_final: 0.7933 (m) REVERT: B 333 CYS cc_start: 0.7273 (t) cc_final: 0.6961 (m) REVERT: B 343 CYS cc_start: 0.8099 (m) cc_final: 0.7831 (m) REVERT: B 378 GLU cc_start: 0.7653 (mp0) cc_final: 0.7414 (mp0) REVERT: B 399 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7321 (pttm) REVERT: B 421 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7801 (mmpt) REVERT: B 428 ASN cc_start: 0.8416 (t0) cc_final: 0.8162 (t0) REVERT: C 82 GLU cc_start: 0.7599 (tp30) cc_final: 0.7248 (tp30) REVERT: C 222 GLU cc_start: 0.8067 (tp30) cc_final: 0.7381 (tp30) REVERT: C 225 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: C 226 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7699 (mmmm) REVERT: C 236 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6851 (mt-10) REVERT: C 289 MET cc_start: 0.8133 (tmm) cc_final: 0.7890 (tmm) REVERT: C 315 LYS cc_start: 0.8196 (tttt) cc_final: 0.7968 (tttt) REVERT: C 338 ASP cc_start: 0.7028 (p0) cc_final: 0.6522 (p0) REVERT: C 373 LEU cc_start: 0.8252 (mt) cc_final: 0.8023 (mp) REVERT: C 399 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7371 (pttm) REVERT: C 422 CYS cc_start: 0.8787 (m) cc_final: 0.8448 (m) REVERT: C 439 CYS cc_start: 0.7659 (p) cc_final: 0.7415 (t) REVERT: C 478 TYR cc_start: 0.7230 (m-10) cc_final: 0.7029 (m-10) outliers start: 65 outliers final: 40 residues processed: 394 average time/residue: 0.2447 time to fit residues: 135.1536 Evaluate side-chains 413 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 366 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 371 ASN 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 421 LYS 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 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 296 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 399 LYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 463 GLU 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 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2638 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= 0.245 Angle : 0.536 7.498 14421 Z= 0.279 Chirality : 0.043 0.311 1743 Planarity : 0.003 0.033 1812 Dihedral : 4.146 19.239 1428 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.72 % Allowed : 27.91 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1344 helix: 1.17 (0.26), residues: 432 sheet: 0.35 (0.29), residues: 327 loop : -1.06 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.003 0.001 HIS C 317 PHE 0.023 0.001 PHE C 509 TYR 0.023 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 452 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 369 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7656 (tp30) cc_final: 0.7229 (tp30) REVERT: A 163 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6691 (mm-30) REVERT: A 232 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: A 318 THR cc_start: 0.8375 (m) cc_final: 0.8068 (p) REVERT: A 378 GLU cc_start: 0.7779 (mp0) cc_final: 0.7397 (mp0) REVERT: A 461 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8125 (mmtt) REVERT: B 30 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: B 82 GLU cc_start: 0.7666 (tp30) cc_final: 0.7365 (tp30) REVERT: B 160 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6660 (mm) REVERT: B 163 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 174 THR cc_start: 0.7851 (t) cc_final: 0.7579 (p) REVERT: B 222 GLU cc_start: 0.8092 (tp30) cc_final: 0.7738 (tp30) REVERT: B 236 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6807 (mt-10) REVERT: B 238 SER cc_start: 0.7928 (t) cc_final: 0.7394 (p) REVERT: B 289 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7946 (tpp) REVERT: B 296 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7666 (m) REVERT: B 313 CYS cc_start: 0.8161 (t) cc_final: 0.7906 (m) REVERT: B 333 CYS cc_start: 0.7196 (t) cc_final: 0.6915 (m) REVERT: B 343 CYS cc_start: 0.8110 (m) cc_final: 0.7815 (m) REVERT: B 378 GLU cc_start: 0.7678 (mp0) cc_final: 0.7472 (mp0) REVERT: B 399 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7500 (pttm) REVERT: B 421 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7774 (mmpt) REVERT: B 428 ASN cc_start: 0.8418 (t0) cc_final: 0.8190 (t0) REVERT: C 82 GLU cc_start: 0.7577 (tp30) cc_final: 0.7254 (tp30) REVERT: C 163 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6784 (mm-30) REVERT: C 174 THR cc_start: 0.7942 (t) cc_final: 0.7573 (p) REVERT: C 222 GLU cc_start: 0.8145 (tp30) cc_final: 0.7528 (tp30) REVERT: C 225 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: C 226 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7924 (mmmm) REVERT: C 236 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6769 (mt-10) REVERT: C 289 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7942 (tmm) REVERT: C 338 ASP cc_start: 0.7027 (p0) cc_final: 0.6561 (p0) REVERT: C 361 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: C 399 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7543 (pttm) REVERT: C 416 CYS cc_start: 0.8388 (p) cc_final: 0.8089 (p) REVERT: C 422 CYS cc_start: 0.8806 (m) cc_final: 0.8496 (m) REVERT: C 439 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7591 (t) outliers start: 83 outliers final: 49 residues processed: 400 average time/residue: 0.2409 time to fit residues: 134.8933 Evaluate side-chains 426 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 365 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 ASP 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 419 LYS Chi-restraints excluded: chain B residue 421 LYS 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 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 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 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 439 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 125 optimal weight: 6.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2715 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 : 0.532 9.341 14421 Z= 0.276 Chirality : 0.042 0.316 1743 Planarity : 0.003 0.033 1812 Dihedral : 4.133 18.286 1428 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.63 % Allowed : 27.99 % Favored : 65.37 % 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: 1.43 (0.27), residues: 414 sheet: 0.32 (0.29), residues: 327 loop : -1.05 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 314 HIS 0.002 0.001 HIS C 317 PHE 0.019 0.001 PHE A 351 TYR 0.023 0.001 TYR B 417 ARG 0.001 0.000 ARG A 336 *********************** 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 455 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 373 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: A 38 SER cc_start: 0.8088 (m) cc_final: 0.7633 (p) REVERT: A 82 GLU cc_start: 0.7657 (tp30) cc_final: 0.7254 (tp30) REVERT: A 163 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6644 (mm-30) REVERT: A 232 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: A 318 THR cc_start: 0.8423 (m) cc_final: 0.8048 (p) REVERT: A 323 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7657 (p) REVERT: A 344 ASP cc_start: 0.7923 (t0) cc_final: 0.7605 (t0) REVERT: A 378 GLU cc_start: 0.7746 (mp0) cc_final: 0.7380 (mp0) REVERT: A 461 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8076 (mmtt) REVERT: B 30 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: B 82 GLU cc_start: 0.7656 (tp30) cc_final: 0.7342 (tp30) REVERT: B 160 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6615 (mm) REVERT: B 163 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6405 (mm-30) REVERT: B 174 THR cc_start: 0.7883 (t) cc_final: 0.7609 (p) REVERT: B 236 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6913 (mt-10) REVERT: B 238 SER cc_start: 0.7942 (t) cc_final: 0.7411 (p) REVERT: B 289 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7902 (tpp) REVERT: B 296 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7661 (m) REVERT: B 313 CYS cc_start: 0.8155 (t) cc_final: 0.7865 (m) REVERT: B 333 CYS cc_start: 0.7150 (t) cc_final: 0.6930 (m) REVERT: B 343 CYS cc_start: 0.8111 (m) cc_final: 0.7836 (m) REVERT: B 352 PHE cc_start: 0.8016 (m-80) cc_final: 0.7752 (m-80) REVERT: B 361 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: B 378 GLU cc_start: 0.7704 (mp0) cc_final: 0.7479 (mp0) REVERT: B 399 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7362 (pttm) REVERT: B 421 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7757 (mmpt) REVERT: B 428 ASN cc_start: 0.8424 (t0) cc_final: 0.8195 (t0) REVERT: C 34 GLN cc_start: 0.8532 (tt0) cc_final: 0.8289 (tt0) REVERT: C 82 GLU cc_start: 0.7578 (tp30) cc_final: 0.7309 (tp30) REVERT: C 163 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6810 (mm-30) REVERT: C 174 THR cc_start: 0.7969 (t) cc_final: 0.7694 (p) REVERT: C 222 GLU cc_start: 0.8122 (tp30) cc_final: 0.7509 (tp30) REVERT: C 225 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: C 226 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7866 (mmmm) REVERT: C 236 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6761 (mt-10) REVERT: C 289 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7912 (tmm) REVERT: C 338 ASP cc_start: 0.6989 (p0) cc_final: 0.6513 (p0) REVERT: C 361 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: C 399 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7503 (pttm) REVERT: C 416 CYS cc_start: 0.8463 (p) cc_final: 0.8152 (p) REVERT: C 422 CYS cc_start: 0.8819 (m) cc_final: 0.8528 (m) outliers start: 82 outliers final: 52 residues processed: 406 average time/residue: 0.2252 time to fit residues: 127.4568 Evaluate side-chains 433 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 367 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 323 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN 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 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 421 LYS 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 505 PHE Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 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 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 463 GLU 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 14 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10644 Z= 0.256 Angle : 0.553 8.552 14421 Z= 0.288 Chirality : 0.043 0.365 1743 Planarity : 0.003 0.033 1812 Dihedral : 4.244 18.158 1428 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: -0.03 (0.23), residues: 1344 helix: 1.15 (0.26), residues: 432 sheet: 0.27 (0.29), residues: 327 loop : -1.05 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 314 HIS 0.002 0.001 HIS B 317 PHE 0.012 0.001 PHE A 509 TYR 0.030 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 460 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 377 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.8032 (m) cc_final: 0.7586 (p) REVERT: A 82 GLU cc_start: 0.7639 (tp30) cc_final: 0.7276 (tp30) REVERT: A 163 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 232 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 236 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 318 THR cc_start: 0.8423 (m) cc_final: 0.8069 (p) REVERT: A 323 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7570 (p) REVERT: A 344 ASP cc_start: 0.7932 (t0) cc_final: 0.7568 (t0) REVERT: A 370 MET cc_start: 0.8449 (ttm) cc_final: 0.8175 (ttm) REVERT: A 378 GLU cc_start: 0.7765 (mp0) cc_final: 0.7395 (mp0) REVERT: A 443 SER cc_start: 0.8564 (p) cc_final: 0.8312 (t) REVERT: A 461 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8053 (mmtt) REVERT: B 30 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: B 82 GLU cc_start: 0.7662 (tp30) cc_final: 0.7399 (tp30) REVERT: B 160 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6608 (mm) REVERT: B 174 THR cc_start: 0.7904 (t) cc_final: 0.7647 (p) REVERT: B 236 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6901 (mt-10) REVERT: B 238 SER cc_start: 0.7992 (t) cc_final: 0.7425 (p) REVERT: B 296 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7714 (m) REVERT: B 313 CYS cc_start: 0.8142 (t) cc_final: 0.7847 (m) REVERT: B 343 CYS cc_start: 0.8095 (m) cc_final: 0.7812 (m) REVERT: B 352 PHE cc_start: 0.8044 (m-80) cc_final: 0.7740 (m-80) REVERT: B 361 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: B 378 GLU cc_start: 0.7692 (mp0) cc_final: 0.7447 (mp0) REVERT: B 399 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7376 (pttm) REVERT: B 417 TYR cc_start: 0.7723 (m-10) cc_final: 0.7495 (m-10) REVERT: B 428 ASN cc_start: 0.8406 (t0) cc_final: 0.8186 (t0) REVERT: C 34 GLN cc_start: 0.8539 (tt0) cc_final: 0.8332 (tt0) REVERT: C 82 GLU cc_start: 0.7571 (tp30) cc_final: 0.7291 (tp30) REVERT: C 174 THR cc_start: 0.7981 (t) cc_final: 0.7739 (p) REVERT: C 222 GLU cc_start: 0.8146 (tp30) cc_final: 0.7552 (tp30) REVERT: C 225 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: C 226 LYS cc_start: 0.8138 (mmmm) cc_final: 0.7910 (mmmm) REVERT: C 236 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6773 (mt-10) REVERT: C 289 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (tmm) REVERT: C 338 ASP cc_start: 0.6985 (p0) cc_final: 0.6494 (p0) REVERT: C 361 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6455 (tt0) REVERT: C 399 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7486 (pttm) REVERT: C 416 CYS cc_start: 0.8364 (p) cc_final: 0.8071 (p) REVERT: C 422 CYS cc_start: 0.8840 (m) cc_final: 0.8519 (m) outliers start: 83 outliers final: 57 residues processed: 407 average time/residue: 0.2270 time to fit residues: 129.4681 Evaluate side-chains 438 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 370 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 323 THR 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 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN 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 399 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 509 PHE Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 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 252 LEU 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 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 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 509 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10644 Z= 0.317 Angle : 0.591 8.235 14421 Z= 0.306 Chirality : 0.045 0.402 1743 Planarity : 0.003 0.033 1812 Dihedral : 4.462 18.753 1428 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.72 % Allowed : 28.64 % Favored : 64.64 % 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: 1.26 (0.27), residues: 414 sheet: 0.18 (0.29), residues: 327 loop : -1.09 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 314 HIS 0.002 0.001 HIS C 317 PHE 0.023 0.001 PHE A 351 TYR 0.031 0.002 TYR B 417 ARG 0.002 0.000 ARG B 336 *********************** 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 460 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 377 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 38 SER cc_start: 0.8037 (m) cc_final: 0.7606 (p) REVERT: A 82 GLU cc_start: 0.7625 (tp30) cc_final: 0.7240 (tp30) REVERT: A 163 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 222 GLU cc_start: 0.7985 (tp30) cc_final: 0.7395 (tp30) REVERT: A 232 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: A 236 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 318 THR cc_start: 0.8420 (m) cc_final: 0.8094 (p) REVERT: A 323 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 344 ASP cc_start: 0.7974 (t0) cc_final: 0.7616 (t0) REVERT: A 378 GLU cc_start: 0.7802 (mp0) cc_final: 0.7434 (mp0) REVERT: A 443 SER cc_start: 0.8536 (p) cc_final: 0.8312 (t) REVERT: A 461 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8136 (mmtt) REVERT: B 30 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 82 GLU cc_start: 0.7657 (tp30) cc_final: 0.7383 (tp30) REVERT: B 160 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6600 (mm) REVERT: B 232 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: B 236 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6984 (mt-10) REVERT: B 238 SER cc_start: 0.8000 (t) cc_final: 0.7448 (p) REVERT: B 296 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7721 (m) REVERT: B 313 CYS cc_start: 0.8089 (t) cc_final: 0.7794 (m) REVERT: B 343 CYS cc_start: 0.8060 (m) cc_final: 0.7746 (m) REVERT: B 352 PHE cc_start: 0.8029 (m-80) cc_final: 0.7795 (m-80) REVERT: B 361 GLN cc_start: 0.7115 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: B 378 GLU cc_start: 0.7694 (mp0) cc_final: 0.7427 (mp0) REVERT: B 399 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7516 (pttm) REVERT: B 428 ASN cc_start: 0.8404 (t0) cc_final: 0.8183 (t0) REVERT: B 439 CYS cc_start: 0.7872 (p) cc_final: 0.7396 (t) REVERT: C 34 GLN cc_start: 0.8582 (tt0) cc_final: 0.8341 (tt0) REVERT: C 82 GLU cc_start: 0.7560 (tp30) cc_final: 0.7295 (tp30) REVERT: C 174 THR cc_start: 0.7998 (t) cc_final: 0.7767 (p) REVERT: C 201 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7408 (mtmt) REVERT: C 222 GLU cc_start: 0.8180 (tp30) cc_final: 0.7629 (tp30) REVERT: C 225 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: C 226 LYS cc_start: 0.8239 (mmmm) cc_final: 0.8009 (mmmm) REVERT: C 232 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: C 236 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6806 (mt-10) REVERT: C 289 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: C 338 ASP cc_start: 0.6956 (p0) cc_final: 0.6500 (p0) REVERT: C 361 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: C 399 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7399 (pttm) REVERT: C 416 CYS cc_start: 0.8325 (p) cc_final: 0.7982 (p) REVERT: C 422 CYS cc_start: 0.8813 (m) cc_final: 0.8508 (m) REVERT: C 439 CYS cc_start: 0.8210 (p) cc_final: 0.7653 (t) outliers start: 83 outliers final: 57 residues processed: 410 average time/residue: 0.2298 time to fit residues: 132.3610 Evaluate side-chains 443 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 373 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ASN 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 30 GLU 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 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN 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 399 LYS Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE 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 264 MET 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0070 chunk 121 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10644 Z= 0.262 Angle : 0.564 7.514 14421 Z= 0.293 Chirality : 0.044 0.427 1743 Planarity : 0.003 0.032 1812 Dihedral : 4.444 19.054 1428 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.83 % Allowed : 29.53 % Favored : 64.64 % 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: 1.29 (0.26), residues: 414 sheet: 0.17 (0.29), residues: 327 loop : -1.11 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 314 HIS 0.002 0.001 HIS A 317 PHE 0.023 0.001 PHE C 509 TYR 0.029 0.002 TYR B 417 ARG 0.002 0.000 ARG B 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 454 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 382 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.7992 (m) cc_final: 0.7532 (p) REVERT: A 82 GLU cc_start: 0.7649 (tp30) cc_final: 0.7235 (tp30) REVERT: A 163 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6615 (mm-30) REVERT: A 222 GLU cc_start: 0.7975 (tp30) cc_final: 0.7374 (tp30) REVERT: A 232 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 236 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 318 THR cc_start: 0.8430 (m) cc_final: 0.8100 (p) REVERT: A 323 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 344 ASP cc_start: 0.7957 (t0) cc_final: 0.7608 (t0) REVERT: A 378 GLU cc_start: 0.7811 (mp0) cc_final: 0.7446 (mp0) REVERT: A 443 SER cc_start: 0.8514 (p) cc_final: 0.8250 (t) REVERT: A 461 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8101 (mmtt) REVERT: B 30 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: B 82 GLU cc_start: 0.7664 (tp30) cc_final: 0.7386 (tp30) REVERT: B 160 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6582 (mm) REVERT: B 236 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6925 (mt-10) REVERT: B 238 SER cc_start: 0.7977 (t) cc_final: 0.7429 (p) REVERT: B 296 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7751 (m) REVERT: B 313 CYS cc_start: 0.8101 (t) cc_final: 0.7792 (m) REVERT: B 343 CYS cc_start: 0.8058 (m) cc_final: 0.7781 (m) REVERT: B 352 PHE cc_start: 0.8039 (m-80) cc_final: 0.7822 (m-80) REVERT: B 361 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: B 378 GLU cc_start: 0.7707 (mp0) cc_final: 0.7431 (mp0) REVERT: B 399 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7421 (pttm) REVERT: B 417 TYR cc_start: 0.7710 (m-10) cc_final: 0.7436 (m-10) REVERT: B 421 LYS cc_start: 0.8055 (mmpt) cc_final: 0.7778 (mmpt) REVERT: B 428 ASN cc_start: 0.8394 (t0) cc_final: 0.8180 (t0) REVERT: B 439 CYS cc_start: 0.7847 (p) cc_final: 0.7506 (t) REVERT: B 444 ASN cc_start: 0.7672 (p0) cc_final: 0.7371 (p0) REVERT: C 34 GLN cc_start: 0.8569 (tt0) cc_final: 0.8324 (tt0) REVERT: C 82 GLU cc_start: 0.7554 (tp30) cc_final: 0.7292 (tp30) REVERT: C 174 THR cc_start: 0.8001 (t) cc_final: 0.7787 (p) REVERT: C 222 GLU cc_start: 0.8179 (tp30) cc_final: 0.7576 (tp30) REVERT: C 225 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: C 226 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7934 (mmmm) REVERT: C 236 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6778 (mt-10) REVERT: C 289 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (tmm) REVERT: C 338 ASP cc_start: 0.6935 (p0) cc_final: 0.6446 (p0) REVERT: C 361 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: C 399 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7348 (pttm) REVERT: C 416 CYS cc_start: 0.8367 (p) cc_final: 0.8074 (p) REVERT: C 422 CYS cc_start: 0.8822 (m) cc_final: 0.8520 (m) REVERT: C 439 CYS cc_start: 0.8029 (p) cc_final: 0.7724 (t) outliers start: 72 outliers final: 58 residues processed: 411 average time/residue: 0.2498 time to fit residues: 144.7673 Evaluate side-chains 444 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 375 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 454 ASN 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 30 GLU 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 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 399 LYS Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 505 PHE Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 509 PHE 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 264 MET 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 425 SER Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 486 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.0170 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3035 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= 0.228 Angle : 0.548 7.384 14421 Z= 0.286 Chirality : 0.043 0.395 1743 Planarity : 0.003 0.032 1812 Dihedral : 4.393 20.743 1428 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.91 % Allowed : 30.02 % Favored : 64.08 % 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: -0.04 (0.23), residues: 1344 helix: 1.33 (0.27), residues: 414 sheet: 0.18 (0.29), residues: 327 loop : -1.10 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 314 HIS 0.002 0.001 HIS A 317 PHE 0.019 0.001 PHE B 351 TYR 0.031 0.001 TYR C 417 ARG 0.002 0.000 ARG B 282 ********************** 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 453 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 380 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 SER cc_start: 0.7957 (m) cc_final: 0.7518 (p) REVERT: A 82 GLU cc_start: 0.7640 (tp30) cc_final: 0.7336 (tp30) REVERT: A 163 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6579 (mm-30) REVERT: A 232 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: A 236 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 318 THR cc_start: 0.8427 (m) cc_final: 0.8091 (p) REVERT: A 344 ASP cc_start: 0.7943 (t0) cc_final: 0.7592 (t0) REVERT: A 378 GLU cc_start: 0.7802 (mp0) cc_final: 0.7439 (mp0) REVERT: A 428 ASN cc_start: 0.8516 (t0) cc_final: 0.8263 (t0) REVERT: A 461 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8100 (mmtt) REVERT: B 30 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: B 82 GLU cc_start: 0.7662 (tp30) cc_final: 0.7373 (tp30) REVERT: B 160 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6590 (mm) REVERT: B 236 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 238 SER cc_start: 0.7984 (t) cc_final: 0.7416 (p) REVERT: B 296 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7707 (m) REVERT: B 352 PHE cc_start: 0.8036 (m-80) cc_final: 0.7720 (m-80) REVERT: B 361 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6534 (tm-30) REVERT: B 378 GLU cc_start: 0.7707 (mp0) cc_final: 0.7451 (mp0) REVERT: B 417 TYR cc_start: 0.7705 (m-10) cc_final: 0.7389 (m-10) REVERT: B 428 ASN cc_start: 0.8398 (t0) cc_final: 0.8189 (t0) REVERT: B 439 CYS cc_start: 0.7753 (p) cc_final: 0.7526 (t) REVERT: C 34 GLN cc_start: 0.8567 (tt0) cc_final: 0.8318 (tt0) REVERT: C 82 GLU cc_start: 0.7525 (tp30) cc_final: 0.7274 (tp30) REVERT: C 174 THR cc_start: 0.7962 (t) cc_final: 0.7678 (p) REVERT: C 201 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7374 (mtmt) REVERT: C 218 GLU cc_start: 0.7772 (mp0) cc_final: 0.7178 (mp0) REVERT: C 222 GLU cc_start: 0.8146 (tp30) cc_final: 0.7507 (tp30) REVERT: C 225 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: C 226 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7834 (mmmm) REVERT: C 236 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6759 (mt-10) REVERT: C 289 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: C 338 ASP cc_start: 0.6915 (p0) cc_final: 0.6418 (p0) REVERT: C 361 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6443 (tt0) REVERT: C 416 CYS cc_start: 0.8315 (p) cc_final: 0.7808 (p) REVERT: C 417 TYR cc_start: 0.7630 (m-10) cc_final: 0.7303 (m-10) REVERT: C 422 CYS cc_start: 0.8797 (m) cc_final: 0.8451 (m) outliers start: 73 outliers final: 57 residues processed: 409 average time/residue: 0.2304 time to fit residues: 131.9551 Evaluate side-chains 439 residues out of total 1236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 374 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 335 THR 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 410 LEU Chi-restraints excluded: chain A residue 454 ASN 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 30 GLU 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 296 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 361 GLN 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 419 LYS Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 509 PHE 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 264 MET 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 402 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 270 GLN B 345 ASN B 437 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** C 437 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113971 restraints weight = 14588.096| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.05 r_work: 0.3235 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10644 Z= 0.155 Angle : 0.522 9.551 14421 Z= 0.272 Chirality : 0.042 0.432 1743 Planarity : 0.003 0.031 1812 Dihedral : 4.200 19.793 1428 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.02 % Allowed : 30.74 % Favored : 64.24 % 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: 1.47 (0.27), residues: 414 sheet: 0.36 (0.29), residues: 324 loop : -1.06 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 32 TYR 0.025 0.001 TYR C 417 ARG 0.001 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3054.29 seconds wall clock time: 56 minutes 30.40 seconds (3390.40 seconds total)