Starting phenix.real_space_refine on Tue Jul 29 02:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3c_36849/07_2025/8k3c_36849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3c_36849/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3c_36849/07_2025/8k3c_36849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3c_36849/07_2025/8k3c_36849.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3c_36849/07_2025/8k3c_36849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3c_36849/07_2025/8k3c_36849.cif" } resolution = 2.88 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.98, per 1000 atoms: 0.74 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: 2.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.92 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: 4.30 Time building geometry restraints manager: 2.81 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: 13.730 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.650 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- 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 : 11.02 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 (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: -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 TRP 0.051 0.005 TRP B 519 HIS 0.013 0.002 HIS A 233 PHE 0.057 0.006 PHE B 364 TYR 0.060 0.005 TYR B 292 ARG 0.014 0.002 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.27380 ( 331) hydrogen bonds : angle 11.06496 ( 999) SS BOND : bond 0.00881 ( 18) SS BOND : angle 1.86666 ( 36) covalent geometry : bond 0.01433 (11078) covalent geometry : angle 1.17096 (15091) *********************** 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 : 1.131 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: 1.0638 time to fit residues: 248.3115 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 : 1.122 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN 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 287 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 195 ASN B 277 ASN B 406 HIS B 478 ASN B 530 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.221944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.173387 restraints weight = 11401.655| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.06 r_work: 0.3871 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11096 Z= 0.179 Angle : 0.667 8.703 15127 Z= 0.352 Chirality : 0.048 0.237 1682 Planarity : 0.006 0.046 1953 Dihedral : 6.633 56.849 1521 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.71 % Allowed : 8.37 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.41 (0.21), residues: 1387 helix: -0.99 (0.57), residues: 67 sheet: -1.49 (0.23), residues: 471 loop : -1.74 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 519 HIS 0.005 0.001 HIS B 233 PHE 0.023 0.003 PHE C 184 TYR 0.028 0.002 TYR A 351 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 331) hydrogen bonds : angle 7.26304 ( 999) SS BOND : bond 0.00360 ( 18) SS BOND : angle 1.23033 ( 36) covalent geometry : bond 0.00411 (11078) covalent geometry : angle 0.66536 (15091) *********************** 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 179 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7668 (m-80) cc_final: 0.6956 (m-80) REVERT: D 55 ARG cc_start: 0.4969 (mtm-85) cc_final: 0.4324 (mtt90) REVERT: D 97 HIS cc_start: 0.6910 (m90) cc_final: 0.6578 (m-70) REVERT: C 30 SER cc_start: 0.5208 (p) cc_final: 0.4697 (t) REVERT: C 34 MET cc_start: 0.7397 (mmm) cc_final: 0.7020 (mmm) REVERT: C 177 LEU cc_start: 0.3816 (tm) cc_final: 0.3049 (mm) REVERT: A 378 ASN cc_start: 0.7344 (t0) cc_final: 0.7084 (t0) REVERT: A 381 ASN cc_start: 0.8303 (m-40) cc_final: 0.8008 (m-40) REVERT: A 391 LYS cc_start: 0.7493 (mtmt) cc_final: 0.7247 (pttm) REVERT: A 402 ARG cc_start: 0.7722 (ptt-90) cc_final: 0.7083 (mtm110) REVERT: A 425 LYS cc_start: 0.7456 (pttt) cc_final: 0.7181 (ptpp) REVERT: A 437 SER cc_start: 0.7488 (p) cc_final: 0.7144 (m) REVERT: A 501 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 554 GLU cc_start: 0.6851 (tt0) cc_final: 0.6408 (tm-30) REVERT: A 589 ARG cc_start: 0.6586 (mtm180) cc_final: 0.5978 (mtp85) REVERT: B 154 LYS cc_start: 0.7292 (mttt) cc_final: 0.6902 (mptt) REVERT: B 191 GLN cc_start: 0.7839 (mp10) cc_final: 0.7142 (mm-40) REVERT: B 254 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7713 (mp0) REVERT: B 374 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 388 GLN cc_start: 0.6964 (mm-40) cc_final: 0.6710 (tm-30) REVERT: B 399 MET cc_start: 0.8369 (mmm) cc_final: 0.7804 (mmm) REVERT: B 519 TRP cc_start: 0.7828 (OUTLIER) cc_final: 0.5408 (t60) REVERT: B 527 ASP cc_start: 0.7133 (t70) cc_final: 0.6804 (t0) REVERT: B 550 GLN cc_start: 0.7460 (pt0) cc_final: 0.7167 (mt0) REVERT: B 569 LYS cc_start: 0.6491 (mtmm) cc_final: 0.5959 (mptt) REVERT: B 599 GLU cc_start: 0.7046 (mp0) cc_final: 0.6811 (tt0) outliers start: 21 outliers final: 7 residues processed: 170 average time/residue: 0.9287 time to fit residues: 174.1538 Evaluate side-chains 127 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 0.6980 chunk 129 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 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 77 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 455 GLN A 518 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.222359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174933 restraints weight = 11599.020| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.91 r_work: 0.3896 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11096 Z= 0.166 Angle : 0.621 8.100 15127 Z= 0.325 Chirality : 0.048 0.278 1682 Planarity : 0.005 0.049 1953 Dihedral : 6.056 66.240 1516 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.60 % Allowed : 10.56 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -2.13 (0.21), residues: 1387 helix: 0.81 (0.71), residues: 54 sheet: -1.34 (0.22), residues: 490 loop : -1.62 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 479 HIS 0.005 0.001 HIS B 233 PHE 0.032 0.002 PHE B 290 TYR 0.034 0.002 TYR C 114 ARG 0.005 0.001 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 331) hydrogen bonds : angle 6.50764 ( 999) SS BOND : bond 0.00423 ( 18) SS BOND : angle 1.08879 ( 36) covalent geometry : bond 0.00383 (11078) covalent geometry : angle 0.61958 (15091) *********************** 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 165 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: D 32 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6476 (m-40) REVERT: D 37 TYR cc_start: 0.7653 (m-80) cc_final: 0.7090 (m-80) REVERT: D 55 ARG cc_start: 0.4950 (mtm-85) cc_final: 0.4235 (mtt90) REVERT: D 97 HIS cc_start: 0.6955 (m90) cc_final: 0.6365 (m90) REVERT: D 139 LEU cc_start: 0.5293 (mm) cc_final: 0.4931 (mm) REVERT: C 177 LEU cc_start: 0.3820 (OUTLIER) cc_final: 0.3092 (mm) REVERT: A 382 CYS cc_start: 0.5808 (t) cc_final: 0.5477 (t) REVERT: A 402 ARG cc_start: 0.7700 (ptt-90) cc_final: 0.7251 (mtm110) REVERT: A 417 ASN cc_start: 0.6074 (t0) cc_final: 0.5855 (t160) REVERT: A 589 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6339 (mtt90) REVERT: B 254 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7553 (mp0) REVERT: B 519 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.6159 (t60) REVERT: B 569 LYS cc_start: 0.6599 (mtmm) cc_final: 0.6089 (mptt) outliers start: 32 outliers final: 12 residues processed: 155 average time/residue: 0.9303 time to fit residues: 159.6914 Evaluate side-chains 127 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 125 THR 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 459 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 519 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 133 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 122 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 93 optimal weight: 0.0670 chunk 44 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 269 ASN A 287 ASN A 543 ASN B 333 HIS B 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.228745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182891 restraints weight = 11427.257| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.95 r_work: 0.4025 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11096 Z= 0.154 Angle : 0.599 8.046 15127 Z= 0.312 Chirality : 0.047 0.173 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.668 49.431 1516 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.92 % Allowed : 11.70 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.97 (0.22), residues: 1387 helix: 1.41 (0.74), residues: 54 sheet: -1.23 (0.22), residues: 499 loop : -1.55 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 519 HIS 0.007 0.001 HIS B 233 PHE 0.044 0.002 PHE D 143 TYR 0.032 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 331) hydrogen bonds : angle 6.24457 ( 999) SS BOND : bond 0.00305 ( 18) SS BOND : angle 1.17627 ( 36) covalent geometry : bond 0.00362 (11078) covalent geometry : angle 0.59650 (15091) *********************** 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 149 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7672 (m-80) cc_final: 0.7205 (m-80) REVERT: D 55 ARG cc_start: 0.4925 (mtm-85) cc_final: 0.4228 (mtt90) REVERT: D 97 HIS cc_start: 0.6807 (m90) cc_final: 0.6228 (m90) REVERT: D 139 LEU cc_start: 0.5258 (mm) cc_final: 0.4874 (mm) REVERT: C 177 LEU cc_start: 0.3884 (OUTLIER) cc_final: 0.3173 (mm) REVERT: A 378 ASN cc_start: 0.7512 (t0) cc_final: 0.7297 (t0) REVERT: A 402 ARG cc_start: 0.7690 (ptt-90) cc_final: 0.7320 (mtm110) REVERT: A 589 ARG cc_start: 0.6742 (mtm180) cc_final: 0.6376 (mtt90) REVERT: B 254 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7597 (mp0) REVERT: B 388 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7379 (pp30) REVERT: B 519 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.6209 (t60) REVERT: B 569 LYS cc_start: 0.6530 (mtmm) cc_final: 0.6035 (mptt) outliers start: 36 outliers final: 22 residues processed: 138 average time/residue: 0.8672 time to fit residues: 133.5518 Evaluate side-chains 128 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 125 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 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 459 SER Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 1 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 HIS C 189 GLN A 509 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.229776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.183363 restraints weight = 11500.419| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.98 r_work: 0.4039 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11096 Z= 0.133 Angle : 0.574 8.581 15127 Z= 0.295 Chirality : 0.046 0.159 1682 Planarity : 0.005 0.050 1953 Dihedral : 5.363 42.649 1516 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.76 % Allowed : 12.59 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.76 (0.22), residues: 1387 helix: 1.82 (0.76), residues: 54 sheet: -1.03 (0.22), residues: 498 loop : -1.48 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 519 HIS 0.007 0.001 HIS B 233 PHE 0.032 0.002 PHE D 143 TYR 0.029 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 331) hydrogen bonds : angle 6.00372 ( 999) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.84451 ( 36) covalent geometry : bond 0.00309 (11078) covalent geometry : angle 0.57351 (15091) *********************** 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 150 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7657 (m-80) cc_final: 0.7158 (m-80) REVERT: D 55 ARG cc_start: 0.4922 (mtm-85) cc_final: 0.4177 (mtt90) REVERT: D 97 HIS cc_start: 0.6575 (m90) cc_final: 0.6034 (m90) REVERT: C 177 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3164 (mm) REVERT: A 378 ASN cc_start: 0.7635 (t0) cc_final: 0.7404 (t0) REVERT: A 402 ARG cc_start: 0.7705 (ptt-90) cc_final: 0.7269 (mtm110) REVERT: A 589 ARG cc_start: 0.6725 (mtm180) cc_final: 0.6351 (mtt90) REVERT: B 254 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7587 (mp0) REVERT: B 399 MET cc_start: 0.8185 (mmm) cc_final: 0.7675 (mmm) REVERT: B 519 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.5878 (t60) REVERT: B 569 LYS cc_start: 0.6528 (mtmm) cc_final: 0.6136 (mptt) outliers start: 34 outliers final: 20 residues processed: 142 average time/residue: 0.8877 time to fit residues: 140.6916 Evaluate side-chains 124 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 125 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 346 ASP Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 430 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN D 171 GLN A 156 HIS A 195 ASN B 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.226736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.180124 restraints weight = 11508.471| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.01 r_work: 0.3992 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11096 Z= 0.190 Angle : 0.624 8.875 15127 Z= 0.320 Chirality : 0.048 0.166 1682 Planarity : 0.005 0.050 1953 Dihedral : 5.427 43.762 1516 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.92 % Allowed : 13.73 % 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 (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: -1.71 (0.22), residues: 1387 helix: 1.49 (0.73), residues: 61 sheet: -0.91 (0.23), residues: 497 loop : -1.50 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 479 HIS 0.005 0.001 HIS B 233 PHE 0.031 0.002 PHE B 290 TYR 0.037 0.002 TYR C 114 ARG 0.004 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 331) hydrogen bonds : angle 6.05070 ( 999) SS BOND : bond 0.00285 ( 18) SS BOND : angle 1.10154 ( 36) covalent geometry : bond 0.00453 (11078) covalent geometry : angle 0.62232 (15091) *********************** 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 135 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7792 (m-80) cc_final: 0.7363 (m-80) REVERT: D 55 ARG cc_start: 0.4916 (mtm-85) cc_final: 0.4139 (mtt90) REVERT: D 97 HIS cc_start: 0.6619 (m90) cc_final: 0.6084 (m90) REVERT: C 177 LEU cc_start: 0.3851 (OUTLIER) cc_final: 0.3089 (mm) REVERT: A 315 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6551 (pmt) REVERT: A 402 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7271 (mtm110) REVERT: A 420 ASP cc_start: 0.6487 (m-30) cc_final: 0.6235 (m-30) REVERT: A 589 ARG cc_start: 0.6938 (mtm180) cc_final: 0.6487 (mtt90) REVERT: B 388 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7361 (pp30) REVERT: B 399 MET cc_start: 0.8339 (mmm) cc_final: 0.7930 (mmm) REVERT: B 519 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.6077 (t60) REVERT: B 569 LYS cc_start: 0.6638 (mtmm) cc_final: 0.6218 (mptt) outliers start: 36 outliers final: 22 residues processed: 128 average time/residue: 0.8783 time to fit residues: 127.1458 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 : 1.243 ------------------------------------------------------------------------------- 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 125 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 315 MET 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 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 388 GLN 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 Chi-restraints excluded: chain B residue 571 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 122 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN B 509 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.230792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184498 restraints weight = 11629.908| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.02 r_work: 0.4048 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11096 Z= 0.120 Angle : 0.564 8.906 15127 Z= 0.289 Chirality : 0.046 0.161 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.124 42.853 1516 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.44 % Allowed : 14.30 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.54 (0.22), residues: 1387 helix: 1.75 (0.73), residues: 61 sheet: -0.78 (0.23), residues: 497 loop : -1.41 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 519 HIS 0.007 0.001 HIS B 233 PHE 0.033 0.002 PHE B 229 TYR 0.034 0.002 TYR C 114 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 331) hydrogen bonds : angle 5.73389 ( 999) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.75660 ( 36) covalent geometry : bond 0.00277 (11078) covalent geometry : angle 0.56301 (15091) *********************** 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 136 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7668 (m-80) cc_final: 0.7205 (m-80) REVERT: D 55 ARG cc_start: 0.4882 (mtm-85) cc_final: 0.4104 (mtt90) REVERT: D 97 HIS cc_start: 0.6403 (m90) cc_final: 0.5880 (m90) REVERT: C 128 THR cc_start: 0.7343 (m) cc_final: 0.6902 (p) REVERT: C 158 CYS cc_start: 0.3563 (OUTLIER) cc_final: 0.3336 (p) REVERT: C 177 LEU cc_start: 0.3963 (OUTLIER) cc_final: 0.3237 (mm) REVERT: A 315 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6115 (pmt) REVERT: A 402 ARG cc_start: 0.7647 (ptt-90) cc_final: 0.7301 (mtm110) REVERT: A 420 ASP cc_start: 0.6488 (m-30) cc_final: 0.6137 (m-30) REVERT: A 589 ARG cc_start: 0.6689 (mtm180) cc_final: 0.6321 (mtt90) REVERT: B 331 ASN cc_start: 0.5716 (m-40) cc_final: 0.5429 (t0) REVERT: B 399 MET cc_start: 0.8222 (mmm) cc_final: 0.7861 (mmm) REVERT: B 519 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.5641 (t60) REVERT: B 569 LYS cc_start: 0.6527 (mtmm) cc_final: 0.6148 (mptt) outliers start: 30 outliers final: 19 residues processed: 130 average time/residue: 0.9601 time to fit residues: 141.6266 Evaluate side-chains 119 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 362 LEU 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 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 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 15 optimal weight: 0.0170 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN D 38 GLN 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 = 0.4655 r_free = 0.4655 target = 0.228478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.182517 restraints weight = 11461.271| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.99 r_work: 0.4012 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11096 Z= 0.164 Angle : 0.613 9.065 15127 Z= 0.312 Chirality : 0.047 0.183 1682 Planarity : 0.005 0.049 1953 Dihedral : 5.206 43.744 1515 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.76 % Allowed : 14.38 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.52 (0.22), residues: 1387 helix: 1.56 (0.72), residues: 61 sheet: -0.70 (0.23), residues: 488 loop : -1.42 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 310 HIS 0.005 0.001 HIS B 233 PHE 0.032 0.002 PHE B 290 TYR 0.030 0.002 TYR C 114 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 331) hydrogen bonds : angle 5.81579 ( 999) SS BOND : bond 0.00279 ( 18) SS BOND : angle 1.64783 ( 36) covalent geometry : bond 0.00395 (11078) covalent geometry : angle 0.60810 (15091) *********************** 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 136 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7726 (m-80) cc_final: 0.7330 (m-80) REVERT: D 55 ARG cc_start: 0.4919 (mtm-85) cc_final: 0.3989 (mtt90) REVERT: D 97 HIS cc_start: 0.6443 (m90) cc_final: 0.5936 (m90) REVERT: C 4 LEU cc_start: 0.5659 (tp) cc_final: 0.5315 (tp) REVERT: C 128 THR cc_start: 0.7362 (m) cc_final: 0.6907 (p) REVERT: C 158 CYS cc_start: 0.3660 (OUTLIER) cc_final: 0.3422 (p) REVERT: C 177 LEU cc_start: 0.3986 (OUTLIER) cc_final: 0.3225 (mm) REVERT: A 315 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6126 (pmt) REVERT: A 402 ARG cc_start: 0.7648 (ptt-90) cc_final: 0.7223 (mtm110) REVERT: A 420 ASP cc_start: 0.6532 (m-30) cc_final: 0.6147 (m-30) REVERT: A 589 ARG cc_start: 0.6754 (mtm180) cc_final: 0.6356 (mtt90) REVERT: B 153 LEU cc_start: 0.7921 (mp) cc_final: 0.7686 (mp) REVERT: B 331 ASN cc_start: 0.5902 (m-40) cc_final: 0.5632 (t0) REVERT: B 399 MET cc_start: 0.8239 (mmm) cc_final: 0.7920 (mmm) REVERT: B 519 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.6077 (t60) REVERT: B 569 LYS cc_start: 0.6580 (mtmm) cc_final: 0.6187 (mptt) outliers start: 34 outliers final: 20 residues processed: 130 average time/residue: 0.8730 time to fit residues: 128.3781 Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 315 MET 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 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 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 90 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 122 optimal weight: 0.0470 chunk 13 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 108 optimal weight: 0.0010 chunk 71 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.7288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 1 GLN C 215 ASN A 156 HIS A 195 ASN B 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.228268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.182099 restraints weight = 11495.740| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 2.00 r_work: 0.4008 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 11096 Z= 0.184 Angle : 0.633 9.297 15127 Z= 0.324 Chirality : 0.048 0.162 1682 Planarity : 0.005 0.051 1953 Dihedral : 5.343 43.939 1515 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.27 % Allowed : 15.11 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.58 (0.22), residues: 1387 helix: 1.43 (0.73), residues: 61 sheet: -0.70 (0.23), residues: 489 loop : -1.48 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 310 HIS 0.005 0.001 HIS B 233 PHE 0.031 0.002 PHE B 290 TYR 0.030 0.002 TYR C 114 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 331) hydrogen bonds : angle 5.85555 ( 999) SS BOND : bond 0.00291 ( 18) SS BOND : angle 1.85800 ( 36) covalent geometry : bond 0.00449 (11078) covalent geometry : angle 0.62702 (15091) *********************** 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 125 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7776 (m-80) cc_final: 0.7411 (m-80) REVERT: D 55 ARG cc_start: 0.4924 (mtm-85) cc_final: 0.3980 (mtt90) REVERT: D 97 HIS cc_start: 0.6483 (m90) cc_final: 0.5988 (m90) REVERT: C 177 LEU cc_start: 0.4078 (OUTLIER) cc_final: 0.3235 (mm) REVERT: A 315 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6369 (pmt) REVERT: A 402 ARG cc_start: 0.7626 (ptt-90) cc_final: 0.7304 (mtm110) REVERT: A 420 ASP cc_start: 0.6628 (m-30) cc_final: 0.6212 (m-30) REVERT: A 530 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6650 (mm-40) REVERT: A 589 ARG cc_start: 0.6858 (mtm180) cc_final: 0.6351 (mtt90) REVERT: B 153 LEU cc_start: 0.7943 (mp) cc_final: 0.7685 (mp) REVERT: B 331 ASN cc_start: 0.6017 (m-40) cc_final: 0.5718 (t0) REVERT: B 399 MET cc_start: 0.8335 (mmm) cc_final: 0.7960 (mmm) REVERT: B 519 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.6170 (t60) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.7563 time to fit residues: 104.9006 Evaluate side-chains 118 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 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 315 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4665 r_free = 0.4665 target = 0.229658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.183746 restraints weight = 11413.598| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.00 r_work: 0.4027 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3724 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= 0.158 Angle : 0.615 8.700 15127 Z= 0.314 Chirality : 0.048 0.165 1682 Planarity : 0.005 0.048 1953 Dihedral : 5.285 43.814 1515 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.11 % Allowed : 15.43 % 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 (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: -1.44 (0.22), residues: 1387 helix: 1.61 (0.73), residues: 61 sheet: -0.59 (0.23), residues: 486 loop : -1.41 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 310 HIS 0.006 0.001 HIS B 233 PHE 0.030 0.002 PHE B 290 TYR 0.030 0.002 TYR C 114 ARG 0.003 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 331) hydrogen bonds : angle 5.77954 ( 999) SS BOND : bond 0.00256 ( 18) SS BOND : angle 1.35261 ( 36) covalent geometry : bond 0.00382 (11078) covalent geometry : angle 0.61186 (15091) ********************** 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 125 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7739 (m-80) cc_final: 0.7345 (m-80) REVERT: D 55 ARG cc_start: 0.4925 (mtm-85) cc_final: 0.3988 (mtt90) REVERT: D 97 HIS cc_start: 0.6438 (m90) cc_final: 0.5914 (m90) REVERT: C 177 LEU cc_start: 0.4126 (OUTLIER) cc_final: 0.3361 (mm) REVERT: A 236 ARG cc_start: 0.6506 (mtt180) cc_final: 0.6301 (ttm170) REVERT: A 315 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6363 (pmt) REVERT: A 402 ARG cc_start: 0.7621 (ptt-90) cc_final: 0.7299 (mtm110) REVERT: A 589 ARG cc_start: 0.6822 (mtm180) cc_final: 0.6330 (mtt90) REVERT: B 153 LEU cc_start: 0.7908 (mp) cc_final: 0.7648 (mt) REVERT: B 331 ASN cc_start: 0.5949 (m-40) cc_final: 0.5632 (t0) REVERT: B 399 MET cc_start: 0.8262 (mmm) cc_final: 0.7878 (mmm) REVERT: B 519 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.6093 (t60) outliers start: 26 outliers final: 20 residues processed: 123 average time/residue: 0.9621 time to fit residues: 132.5617 Evaluate side-chains 116 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 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 315 MET 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 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 130 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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 = 0.4685 r_free = 0.4685 target = 0.232065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.186799 restraints weight = 11439.569| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 2.00 r_work: 0.4059 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11096 Z= 0.130 Angle : 0.597 8.724 15127 Z= 0.304 Chirality : 0.047 0.167 1682 Planarity : 0.005 0.048 1953 Dihedral : 5.173 43.274 1515 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.79 % Allowed : 16.33 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % 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: -1.30 (0.22), residues: 1387 helix: 1.78 (0.73), residues: 61 sheet: -0.42 (0.24), residues: 476 loop : -1.37 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 310 HIS 0.008 0.001 HIS B 233 PHE 0.042 0.002 PHE D 143 TYR 0.032 0.002 TYR C 114 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 331) hydrogen bonds : angle 5.65356 ( 999) SS BOND : bond 0.00206 ( 18) SS BOND : angle 1.23915 ( 36) covalent geometry : bond 0.00309 (11078) covalent geometry : angle 0.59438 (15091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9366.37 seconds wall clock time: 161 minutes 55.57 seconds (9715.57 seconds total)