Starting phenix.real_space_refine on Sat Aug 23 08:41:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3c_36849/08_2025/8k3c_36849.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 61 5.16 5 C 6844 2.51 5 N 1824 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10813 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Chain: "C" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1778 Classifications: {'peptide': 238} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 224} Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3710 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 437} Chain: "B" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3718 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 438} Time building chain proxies: 2.60, per 1000 atoms: 0.24 Number of scatterers: 10813 At special positions: 0 Unit cell: (95.12, 109.88, 176.3, 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 61 16.00 O 2084 8.00 N 1824 7.00 C 6844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 197 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.02 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.01 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.02 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.02 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: 0.85 Conformation dependent library (CDL) restraints added in 442.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 27 sheets defined 7.5% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 125 through 131 removed outlier: 4.222A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.352A pdb=" N SER C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.605A pdb=" N CYS B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.269A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 118 through 121 removed outlier: 3.696A pdb=" N LEU D 182 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP D 142 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR D 176 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.888A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.514A pdb=" N THR C 125 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.830A pdb=" N TYR C 194 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.765A pdb=" N CYS C 214 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS C 227 " --> pdb=" O CYS C 214 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 216 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.744A pdb=" N LYS A 199 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS A 596 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 216 through 224 removed outlier: 6.282A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET A 224 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TYR A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.286A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB7, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.800A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 465 " --> pdb=" O GLN A 455 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.590A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 557 through 567 removed outlier: 3.922A pdb=" N ASN A 557 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU A 579 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR A 561 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 577 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR A 563 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 575 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 565 " --> pdb=" O TRP A 573 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP A 573 " --> pdb=" O CYS A 565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 178 through 179 removed outlier: 5.965A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 587 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.557A pdb=" N PHE B 229 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.398A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 340 through 341 removed outlier: 3.808A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AC8, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.512A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 465 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 511 through 513 removed outlier: 4.971A pdb=" N GLN B 550 " --> pdb=" O PRO B 535 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE B 537 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 999 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: 1.50 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3412 1.34 - 1.46: 2844 1.46 - 1.59: 4744 1.59 - 1.72: 0 1.72 - 1.84: 78 Bond restraints: 11078 Sorted by residual: bond pdb=" C SER A 390 " pdb=" N LYS A 391 " ideal model delta sigma weight residual 1.329 1.237 0.091 1.60e-02 3.91e+03 3.25e+01 bond pdb=" N GLN D 112 " pdb=" CA GLN D 112 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N ILE D 140 " pdb=" CA ILE D 140 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N VAL D 119 " pdb=" CA VAL D 119 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" CB ILE A 356 " pdb=" CG2 ILE A 356 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.06e+00 ... (remaining 11073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 14692 3.11 - 6.22: 365 6.22 - 9.33: 29 9.33 - 12.44: 4 12.44 - 15.55: 1 Bond angle restraints: 15091 Sorted by residual: angle pdb=" N PRO D 123 " pdb=" CA PRO D 123 " pdb=" C PRO D 123 " ideal model delta sigma weight residual 110.70 117.59 -6.89 1.22e+00 6.72e-01 3.19e+01 angle pdb=" CA TYR C 114 " pdb=" CB TYR C 114 " pdb=" CG TYR C 114 " ideal model delta sigma weight residual 113.90 123.60 -9.70 1.80e+00 3.09e-01 2.91e+01 angle pdb=" C THR B 218 " pdb=" N ASP B 219 " pdb=" CA ASP B 219 " ideal model delta sigma weight residual 122.83 128.51 -5.68 1.08e+00 8.57e-01 2.76e+01 angle pdb=" CB MET B 267 " pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 112.70 97.15 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C THR C 237 " pdb=" N SER C 238 " pdb=" CA SER C 238 " ideal model delta sigma weight residual 121.70 130.89 -9.19 1.80e+00 3.09e-01 2.61e+01 ... (remaining 15086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6390 17.73 - 35.46: 244 35.46 - 53.19: 62 53.19 - 70.92: 5 70.92 - 88.65: 4 Dihedral angle restraints: 6705 sinusoidal: 2653 harmonic: 4052 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual -86.00 -174.65 88.65 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual 93.00 165.03 -72.03 1 1.00e+01 1.00e-02 6.64e+01 dihedral pdb=" CA GLY C 53 " pdb=" C GLY C 53 " pdb=" N SER C 54 " pdb=" CA SER C 54 " ideal model delta harmonic sigma weight residual -180.00 -140.63 -39.37 0 5.00e+00 4.00e-02 6.20e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1279 0.075 - 0.149: 356 0.149 - 0.224: 37 0.224 - 0.298: 8 0.298 - 0.373: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CB ILE B 444 " pdb=" CA ILE B 444 " pdb=" CG1 ILE B 444 " pdb=" CG2 ILE B 444 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB ILE A 444 " pdb=" CA ILE A 444 " pdb=" CG1 ILE A 444 " pdb=" CG2 ILE A 444 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1679 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 292 " -0.029 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR B 292 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 292 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 292 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 292 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 292 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 292 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 168 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C PHE B 168 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE B 168 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 169 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " -0.019 2.00e-02 2.50e+03 2.37e-02 1.12e+01 pdb=" CG TYR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " -0.000 2.00e-02 2.50e+03 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 476 2.69 - 3.24: 10072 3.24 - 3.80: 18651 3.80 - 4.35: 23532 4.35 - 4.90: 39709 Nonbonded interactions: 92440 Sorted by model distance: nonbonded pdb=" CB ALA D 115 " pdb=" N TYR D 144 " model vdw 2.138 3.540 nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 528 " pdb=" O THR A 531 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 205 " pdb=" OH TYR A 231 " model vdw 2.224 3.040 nonbonded pdb=" OG SER B 298 " pdb=" O GLY B 301 " model vdw 2.261 3.040 ... (remaining 92435 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' and resid 132 through 601) } 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=0.00 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: 10.240 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.210 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.014 0.118 11096 Z= 0.623 Angle : 1.173 15.554 15127 Z= 0.660 Chirality : 0.067 0.373 1682 Planarity : 0.008 0.068 1953 Dihedral : 10.350 79.053 4057 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer: Outliers : 0.57 % Allowed : 2.44 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.08 (0.20), residues: 1387 helix: -1.99 (0.50), residues: 66 sheet: -1.94 (0.22), residues: 476 loop : -2.15 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 487 TYR 0.060 0.005 TYR B 292 PHE 0.057 0.006 PHE B 364 TRP 0.051 0.005 TRP B 519 HIS 0.013 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.01433 (11078) covalent geometry : angle 1.17096 (15091) SS BOND : bond 0.00881 ( 18) SS BOND : angle 1.86666 ( 36) hydrogen bonds : bond 0.27380 ( 331) hydrogen bonds : angle 11.06496 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 ARG cc_start: 0.4668 (mtm-85) cc_final: 0.3794 (mtt-85) REVERT: D 97 HIS cc_start: 0.6829 (m90) cc_final: 0.6440 (m-70) REVERT: D 212 PRO cc_start: 0.4885 (Cg_endo) cc_final: 0.4684 (Cg_exo) REVERT: C 34 MET cc_start: 0.6443 (mmm) cc_final: 0.5865 (mmm) REVERT: C 39 GLN cc_start: 0.5983 (tt0) cc_final: 0.5643 (tt0) REVERT: C 93 VAL cc_start: 0.6082 (t) cc_final: 0.5814 (p) REVERT: C 197 SER cc_start: 0.6115 (m) cc_final: 0.5707 (t) REVERT: A 381 ASN cc_start: 0.8349 (m-40) cc_final: 0.7991 (m-40) REVERT: A 391 LYS cc_start: 0.7348 (mtmt) cc_final: 0.6985 (ptpp) REVERT: A 425 LYS cc_start: 0.7135 (pttt) cc_final: 0.6869 (ptpp) REVERT: A 437 SER cc_start: 0.7316 (p) cc_final: 0.6947 (m) REVERT: A 501 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5945 (mm-30) REVERT: A 554 GLU cc_start: 0.6248 (tt0) cc_final: 0.5647 (tm-30) REVERT: A 589 ARG cc_start: 0.5795 (mtm180) cc_final: 0.4935 (mtp85) REVERT: B 199 LYS cc_start: 0.8082 (mttt) cc_final: 0.7678 (mmtp) REVERT: B 254 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6777 (mp0) REVERT: B 374 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6868 (mt-10) REVERT: B 388 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6607 (tm-30) REVERT: B 389 TYR cc_start: 0.7984 (m-10) cc_final: 0.7295 (m-80) REVERT: B 399 MET cc_start: 0.7924 (mmm) cc_final: 0.7581 (mmm) REVERT: B 519 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6391 (t60) REVERT: B 527 ASP cc_start: 0.6327 (t70) cc_final: 0.6066 (t0) REVERT: B 550 GLN cc_start: 0.6973 (pt0) cc_final: 0.6334 (tt0) REVERT: B 569 LYS cc_start: 0.6103 (mtmm) cc_final: 0.5503 (mptt) REVERT: B 588 ILE cc_start: 0.7546 (mt) cc_final: 0.7099 (tp) REVERT: B 599 GLU cc_start: 0.6789 (mp0) cc_final: 0.6512 (tt0) outliers start: 7 outliers final: 5 residues processed: 214 average time/residue: 0.4361 time to fit residues: 101.6627 Evaluate side-chains 126 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN D 39 GLN C 82 GLN C 123 GLN C 189 GLN A 139 ASN A 159 ASN A 164 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN A 269 ASN A 306 ASN A 333 HIS A 406 HIS A 423 ASN A 434 GLN A 529 ASN A 557 ASN B 141 ASN B 156 HIS B 277 ASN B 406 HIS B 478 ASN B 530 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.223003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.174634 restraints weight = 11536.875| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.07 r_work: 0.3879 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11096 Z= 0.166 Angle : 0.660 8.693 15127 Z= 0.348 Chirality : 0.048 0.270 1682 Planarity : 0.006 0.046 1953 Dihedral : 6.616 56.553 1521 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.46 % Allowed : 8.53 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.21), residues: 1387 helix: -1.07 (0.56), residues: 67 sheet: -1.51 (0.22), residues: 471 loop : -1.73 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 372 TYR 0.029 0.002 TYR A 351 PHE 0.025 0.003 PHE C 184 TRP 0.020 0.002 TRP A 519 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00372 (11078) covalent geometry : angle 0.65761 (15091) SS BOND : bond 0.00265 ( 18) SS BOND : angle 1.22116 ( 36) hydrogen bonds : bond 0.04528 ( 331) hydrogen bonds : angle 7.25691 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7565 (m-80) cc_final: 0.6870 (m-80) REVERT: D 55 ARG cc_start: 0.4929 (mtm-85) cc_final: 0.4249 (mtt90) REVERT: D 70 THR cc_start: 0.8099 (p) cc_final: 0.7684 (t) REVERT: D 97 HIS cc_start: 0.6937 (m90) cc_final: 0.6598 (m-70) REVERT: C 30 SER cc_start: 0.5199 (p) cc_final: 0.4688 (t) REVERT: C 34 MET cc_start: 0.7384 (mmm) cc_final: 0.7027 (mmm) REVERT: C 177 LEU cc_start: 0.3607 (tm) cc_final: 0.2884 (mm) REVERT: A 378 ASN cc_start: 0.7209 (t0) cc_final: 0.6973 (t0) REVERT: A 381 ASN cc_start: 0.8292 (m-40) cc_final: 0.7994 (m-40) REVERT: A 391 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7261 (pttm) REVERT: A 402 ARG cc_start: 0.7717 (ptt-90) cc_final: 0.7090 (mtm110) REVERT: A 425 LYS cc_start: 0.7433 (pttt) cc_final: 0.7171 (ptpp) REVERT: A 437 SER cc_start: 0.7373 (p) cc_final: 0.7170 (m) REVERT: A 501 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6751 (mm-30) REVERT: A 554 GLU cc_start: 0.6836 (tt0) cc_final: 0.6408 (tm-30) REVERT: A 589 ARG cc_start: 0.6533 (mtm180) cc_final: 0.5956 (mtp85) REVERT: B 191 GLN cc_start: 0.7826 (mp10) cc_final: 0.7135 (mm-40) REVERT: B 225 ASP cc_start: 0.5719 (t0) cc_final: 0.5511 (t0) REVERT: B 254 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7702 (mp0) REVERT: B 374 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 388 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6708 (tm-30) REVERT: B 399 MET cc_start: 0.8374 (mmm) cc_final: 0.7802 (mmm) REVERT: B 519 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.5423 (t60) REVERT: B 527 ASP cc_start: 0.7099 (t70) cc_final: 0.6780 (t0) REVERT: B 550 GLN cc_start: 0.7500 (pt0) cc_final: 0.7199 (mt0) REVERT: B 569 LYS cc_start: 0.6478 (mtmm) cc_final: 0.5954 (mptt) REVERT: B 599 GLU cc_start: 0.7039 (mp0) cc_final: 0.6823 (tt0) outliers start: 18 outliers final: 6 residues processed: 173 average time/residue: 0.3980 time to fit residues: 75.9582 Evaluate side-chains 127 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.0040 chunk 64 optimal weight: 2.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 52 ASN D 171 GLN C 77 ASN A 388 GLN A 455 GLN A 518 ASN B 156 HIS B 333 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.220306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171660 restraints weight = 11486.514| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.92 r_work: 0.3816 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11096 Z= 0.208 Angle : 0.659 9.105 15127 Z= 0.345 Chirality : 0.049 0.275 1682 Planarity : 0.005 0.049 1953 Dihedral : 6.233 68.217 1516 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.60 % Allowed : 10.32 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.21), residues: 1387 helix: 0.07 (0.67), residues: 60 sheet: -1.39 (0.22), residues: 490 loop : -1.65 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 589 TYR 0.034 0.002 TYR C 114 PHE 0.030 0.003 PHE B 290 TRP 0.023 0.002 TRP A 519 HIS 0.005 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00493 (11078) covalent geometry : angle 0.65743 (15091) SS BOND : bond 0.00346 ( 18) SS BOND : angle 1.25011 ( 36) hydrogen bonds : bond 0.04215 ( 331) hydrogen bonds : angle 6.74005 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7724 (m-80) cc_final: 0.7122 (m-80) REVERT: D 55 ARG cc_start: 0.5055 (mtm-85) cc_final: 0.4337 (mtt90) REVERT: D 97 HIS cc_start: 0.7056 (m90) cc_final: 0.6445 (m90) REVERT: C 30 SER cc_start: 0.5109 (p) cc_final: 0.4648 (t) REVERT: C 177 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3094 (mm) REVERT: A 382 CYS cc_start: 0.5934 (t) cc_final: 0.5603 (t) REVERT: A 402 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7318 (mtm110) REVERT: A 420 ASP cc_start: 0.6136 (m-30) cc_final: 0.5863 (m-30) REVERT: A 554 GLU cc_start: 0.6979 (tt0) cc_final: 0.6758 (tm-30) REVERT: A 589 ARG cc_start: 0.6835 (mtm180) cc_final: 0.6373 (mtt90) REVERT: B 191 GLN cc_start: 0.7689 (mt0) cc_final: 0.7194 (mm-40) REVERT: B 254 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 519 TRP cc_start: 0.8061 (OUTLIER) cc_final: 0.6298 (t60) REVERT: B 569 LYS cc_start: 0.6579 (mtmm) cc_final: 0.6112 (mptt) outliers start: 32 outliers final: 14 residues processed: 150 average time/residue: 0.4085 time to fit residues: 67.8371 Evaluate side-chains 122 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 0.0050 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 108 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 192 HIS A 543 ASN B 334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.226193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.179474 restraints weight = 11565.074| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.04 r_work: 0.3966 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11096 Z= 0.157 Angle : 0.597 6.948 15127 Z= 0.312 Chirality : 0.047 0.198 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.682 44.362 1516 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.68 % Allowed : 11.78 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.22), residues: 1387 helix: 1.32 (0.74), residues: 54 sheet: -1.26 (0.22), residues: 499 loop : -1.55 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.032 0.002 TYR C 114 PHE 0.032 0.002 PHE B 229 TRP 0.012 0.002 TRP A 479 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00362 (11078) covalent geometry : angle 0.59508 (15091) SS BOND : bond 0.00321 ( 18) SS BOND : angle 1.23841 ( 36) hydrogen bonds : bond 0.03661 ( 331) hydrogen bonds : angle 6.29137 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7686 (m-80) cc_final: 0.7260 (m-80) REVERT: D 55 ARG cc_start: 0.4951 (mtm-85) cc_final: 0.4237 (mtt90) REVERT: D 97 HIS cc_start: 0.6847 (m90) cc_final: 0.6284 (m90) REVERT: C 163 TYR cc_start: 0.5290 (p90) cc_final: 0.4558 (p90) REVERT: C 177 LEU cc_start: 0.3793 (OUTLIER) cc_final: 0.3057 (mm) REVERT: A 291 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 378 ASN cc_start: 0.7456 (t0) cc_final: 0.7146 (t0) REVERT: A 402 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7372 (mtm110) REVERT: A 589 ARG cc_start: 0.6829 (mtm180) cc_final: 0.6412 (mtt90) REVERT: B 254 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 388 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7386 (pp30) REVERT: B 519 TRP cc_start: 0.7966 (OUTLIER) cc_final: 0.5871 (t60) REVERT: B 569 LYS cc_start: 0.6562 (mtmm) cc_final: 0.6155 (mptt) outliers start: 33 outliers final: 19 residues processed: 142 average time/residue: 0.3762 time to fit residues: 59.5884 Evaluate side-chains 123 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 509 ASN B 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.224971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.177975 restraints weight = 11509.103| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.87 r_work: 0.3981 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11096 Z= 0.215 Angle : 0.643 7.689 15127 Z= 0.333 Chirality : 0.049 0.170 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.653 43.964 1516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.92 % Allowed : 12.51 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.22), residues: 1387 helix: 1.27 (0.71), residues: 60 sheet: -1.10 (0.22), residues: 498 loop : -1.59 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 487 TYR 0.027 0.002 TYR C 114 PHE 0.045 0.003 PHE D 143 TRP 0.013 0.002 TRP A 519 HIS 0.008 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00515 (11078) covalent geometry : angle 0.64147 (15091) SS BOND : bond 0.00340 ( 18) SS BOND : angle 1.19832 ( 36) hydrogen bonds : bond 0.03892 ( 331) hydrogen bonds : angle 6.35076 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7775 (m-80) cc_final: 0.7429 (m-80) REVERT: D 55 ARG cc_start: 0.4965 (mtm-85) cc_final: 0.4076 (mtt90) REVERT: D 97 HIS cc_start: 0.6855 (m90) cc_final: 0.6325 (m90) REVERT: A 402 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7266 (mtm110) REVERT: A 589 ARG cc_start: 0.6977 (mtm180) cc_final: 0.6557 (mtt90) REVERT: B 519 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.6163 (t60) REVERT: B 569 LYS cc_start: 0.6693 (mtmm) cc_final: 0.6275 (mptt) outliers start: 36 outliers final: 22 residues processed: 135 average time/residue: 0.3598 time to fit residues: 53.9416 Evaluate side-chains 124 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 94 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN C 189 GLN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.227725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.180878 restraints weight = 11479.412| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.03 r_work: 0.4014 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11096 Z= 0.158 Angle : 0.597 7.738 15127 Z= 0.307 Chirality : 0.047 0.163 1682 Planarity : 0.005 0.048 1953 Dihedral : 5.387 43.569 1516 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.84 % Allowed : 13.00 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.22), residues: 1387 helix: 1.51 (0.72), residues: 61 sheet: -0.94 (0.23), residues: 498 loop : -1.52 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.021 0.002 TYR B 345 PHE 0.036 0.002 PHE D 143 TRP 0.013 0.002 TRP A 519 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00374 (11078) covalent geometry : angle 0.59588 (15091) SS BOND : bond 0.00232 ( 18) SS BOND : angle 0.91970 ( 36) hydrogen bonds : bond 0.03512 ( 331) hydrogen bonds : angle 6.05480 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6380 (m110) REVERT: D 37 TYR cc_start: 0.7756 (m-80) cc_final: 0.7260 (m-80) REVERT: D 55 ARG cc_start: 0.4893 (mtm-85) cc_final: 0.3987 (mtt90) REVERT: D 97 HIS cc_start: 0.6737 (m90) cc_final: 0.6222 (m90) REVERT: C 177 LEU cc_start: 0.3792 (OUTLIER) cc_final: 0.3070 (mm) REVERT: A 378 ASN cc_start: 0.7530 (t0) cc_final: 0.7329 (t0) REVERT: A 382 CYS cc_start: 0.5614 (t) cc_final: 0.5357 (t) REVERT: A 402 ARG cc_start: 0.7670 (ptt-90) cc_final: 0.7339 (mtm110) REVERT: A 589 ARG cc_start: 0.6912 (mtm180) cc_final: 0.6469 (mtt90) REVERT: B 153 LEU cc_start: 0.7940 (mp) cc_final: 0.7723 (mp) REVERT: B 519 TRP cc_start: 0.8045 (OUTLIER) cc_final: 0.5911 (t60) outliers start: 35 outliers final: 23 residues processed: 136 average time/residue: 0.3596 time to fit residues: 54.8419 Evaluate side-chains 121 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 46 optimal weight: 0.1980 chunk 63 optimal weight: 0.0010 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 137 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN B 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.228669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.182469 restraints weight = 11447.280| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.91 r_work: 0.4028 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11096 Z= 0.141 Angle : 0.586 8.007 15127 Z= 0.300 Chirality : 0.047 0.183 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.258 43.491 1516 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.68 % Allowed : 13.97 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.22), residues: 1387 helix: 1.71 (0.73), residues: 61 sheet: -0.87 (0.23), residues: 498 loop : -1.47 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.021 0.002 TYR C 115 PHE 0.031 0.002 PHE D 143 TRP 0.012 0.001 TRP A 519 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00329 (11078) covalent geometry : angle 0.58560 (15091) SS BOND : bond 0.00205 ( 18) SS BOND : angle 0.79153 ( 36) hydrogen bonds : bond 0.03395 ( 331) hydrogen bonds : angle 5.96009 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7687 (m-80) cc_final: 0.7351 (m-80) REVERT: D 55 ARG cc_start: 0.4906 (mtm-85) cc_final: 0.3980 (mtt90) REVERT: D 97 HIS cc_start: 0.6628 (m90) cc_final: 0.6135 (m90) REVERT: C 177 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3217 (mm) REVERT: A 378 ASN cc_start: 0.7580 (t0) cc_final: 0.7341 (t0) REVERT: A 382 CYS cc_start: 0.5634 (t) cc_final: 0.5385 (t) REVERT: A 402 ARG cc_start: 0.7666 (ptt-90) cc_final: 0.7326 (mtm110) REVERT: A 589 ARG cc_start: 0.6744 (mtm180) cc_final: 0.6340 (mtt90) REVERT: B 153 LEU cc_start: 0.7931 (mp) cc_final: 0.7678 (mp) REVERT: B 254 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7564 (mp0) REVERT: B 519 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.5888 (t60) outliers start: 33 outliers final: 22 residues processed: 129 average time/residue: 0.3146 time to fit residues: 45.7537 Evaluate side-chains 119 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 49 optimal weight: 0.2980 chunk 44 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.231205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.185648 restraints weight = 11559.247| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.91 r_work: 0.4062 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11096 Z= 0.120 Angle : 0.577 9.209 15127 Z= 0.294 Chirality : 0.047 0.169 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.094 43.146 1515 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.36 % Allowed : 14.87 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.22), residues: 1387 helix: 1.88 (0.73), residues: 61 sheet: -0.76 (0.23), residues: 488 loop : -1.42 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 487 TYR 0.020 0.001 TYR C 115 PHE 0.030 0.002 PHE B 290 TRP 0.015 0.001 TRP A 310 HIS 0.009 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00278 (11078) covalent geometry : angle 0.57683 (15091) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.73194 ( 36) hydrogen bonds : bond 0.03182 ( 331) hydrogen bonds : angle 5.77280 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7735 (m-80) cc_final: 0.7353 (m-80) REVERT: D 55 ARG cc_start: 0.4842 (mtm-85) cc_final: 0.4050 (mtt90) REVERT: D 97 HIS cc_start: 0.6507 (m90) cc_final: 0.6001 (m90) REVERT: C 30 SER cc_start: 0.5326 (p) cc_final: 0.5118 (t) REVERT: C 177 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3196 (mm) REVERT: A 382 CYS cc_start: 0.5578 (t) cc_final: 0.5339 (t) REVERT: A 402 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.7284 (mtm110) REVERT: A 589 ARG cc_start: 0.6679 (mtm180) cc_final: 0.6254 (mtt90) REVERT: B 153 LEU cc_start: 0.7874 (mp) cc_final: 0.7625 (mp) REVERT: B 191 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: B 254 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7530 (mp0) REVERT: B 331 ASN cc_start: 0.5832 (m-40) cc_final: 0.5515 (t0) REVERT: B 519 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.5718 (t60) REVERT: B 569 LYS cc_start: 0.6545 (mtmm) cc_final: 0.6174 (mptt) outliers start: 29 outliers final: 21 residues processed: 139 average time/residue: 0.3585 time to fit residues: 55.7203 Evaluate side-chains 122 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN C 77 ASN A 156 HIS A 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.226699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.179793 restraints weight = 11377.516| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 1.92 r_work: 0.4002 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11096 Z= 0.198 Angle : 0.634 8.426 15127 Z= 0.323 Chirality : 0.048 0.166 1682 Planarity : 0.005 0.055 1953 Dihedral : 5.284 44.252 1515 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.52 % Allowed : 15.03 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.22), residues: 1387 helix: 1.79 (0.73), residues: 61 sheet: -0.62 (0.23), residues: 481 loop : -1.47 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 480 TYR 0.023 0.002 TYR B 345 PHE 0.031 0.002 PHE B 290 TRP 0.019 0.002 TRP A 310 HIS 0.003 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00477 (11078) covalent geometry : angle 0.63141 (15091) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.24037 ( 36) hydrogen bonds : bond 0.03515 ( 331) hydrogen bonds : angle 5.95637 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7767 (m-80) cc_final: 0.7424 (m-80) REVERT: D 55 ARG cc_start: 0.4940 (mtm-85) cc_final: 0.3992 (mtt90) REVERT: D 97 HIS cc_start: 0.6575 (m90) cc_final: 0.6093 (m90) REVERT: D 106 LYS cc_start: 0.6626 (tptp) cc_final: 0.6090 (tptt) REVERT: C 177 LEU cc_start: 0.4069 (OUTLIER) cc_final: 0.3211 (mm) REVERT: A 402 ARG cc_start: 0.7651 (ptt-90) cc_final: 0.7235 (mtm110) REVERT: A 571 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6591 (mptm) REVERT: A 589 ARG cc_start: 0.6762 (mtm180) cc_final: 0.6342 (mtt90) REVERT: B 153 LEU cc_start: 0.7902 (mp) cc_final: 0.7608 (mt) REVERT: B 519 TRP cc_start: 0.8070 (OUTLIER) cc_final: 0.6203 (t60) REVERT: B 569 LYS cc_start: 0.6675 (mtmm) cc_final: 0.6237 (mptt) outliers start: 31 outliers final: 23 residues processed: 129 average time/residue: 0.3133 time to fit residues: 46.0251 Evaluate side-chains 120 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 131 optimal weight: 0.0570 chunk 85 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN A 156 HIS A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.227743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181267 restraints weight = 11448.733| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.90 r_work: 0.4017 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3913 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11096 Z= 0.167 Angle : 0.621 7.823 15127 Z= 0.317 Chirality : 0.047 0.155 1682 Planarity : 0.005 0.051 1953 Dihedral : 5.276 44.023 1515 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.11 % Allowed : 15.76 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.22), residues: 1387 helix: 1.84 (0.74), residues: 61 sheet: -0.63 (0.23), residues: 483 loop : -1.42 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 487 TYR 0.021 0.002 TYR B 345 PHE 0.031 0.002 PHE B 290 TRP 0.020 0.002 TRP A 310 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00401 (11078) covalent geometry : angle 0.62023 (15091) SS BOND : bond 0.00250 ( 18) SS BOND : angle 1.01355 ( 36) hydrogen bonds : bond 0.03382 ( 331) hydrogen bonds : angle 5.89507 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7818 (m-80) cc_final: 0.7413 (m-80) REVERT: D 55 ARG cc_start: 0.4901 (mtm-85) cc_final: 0.3963 (mtt90) REVERT: D 97 HIS cc_start: 0.6554 (m90) cc_final: 0.6076 (m90) REVERT: C 177 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3196 (mm) REVERT: A 402 ARG cc_start: 0.7636 (ptt-90) cc_final: 0.7314 (mtm110) REVERT: A 571 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6557 (mptm) REVERT: A 589 ARG cc_start: 0.6747 (mtm180) cc_final: 0.6303 (mtt90) REVERT: B 153 LEU cc_start: 0.7864 (mp) cc_final: 0.7568 (mt) REVERT: B 331 ASN cc_start: 0.5946 (m-40) cc_final: 0.5651 (t0) REVERT: B 519 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.6024 (t60) REVERT: B 569 LYS cc_start: 0.6656 (mtmm) cc_final: 0.6221 (mptt) outliers start: 26 outliers final: 21 residues processed: 120 average time/residue: 0.3230 time to fit residues: 43.9237 Evaluate side-chains 117 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 561 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 1 GLN A 156 HIS A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.225460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.178626 restraints weight = 11525.800| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 1.94 r_work: 0.3987 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11096 Z= 0.209 Angle : 0.656 7.904 15127 Z= 0.336 Chirality : 0.049 0.167 1682 Planarity : 0.005 0.063 1953 Dihedral : 5.430 44.892 1515 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.44 % Allowed : 15.60 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.22), residues: 1387 helix: 2.10 (0.78), residues: 55 sheet: -0.58 (0.23), residues: 483 loop : -1.48 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 487 TYR 0.027 0.002 TYR B 345 PHE 0.033 0.003 PHE B 290 TRP 0.022 0.002 TRP A 310 HIS 0.003 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00507 (11078) covalent geometry : angle 0.65371 (15091) SS BOND : bond 0.00316 ( 18) SS BOND : angle 1.27123 ( 36) hydrogen bonds : bond 0.03612 ( 331) hydrogen bonds : angle 6.05120 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.04 seconds wall clock time: 67 minutes 56.32 seconds (4076.32 seconds total)