Starting phenix.real_space_refine on Mon Aug 25 16:22:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4k_17410/08_2025/8p4k_17410.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.205 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: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 9369 2.51 5 N 2409 2.21 5 O 2712 1.98 5 H 14643 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29211 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9737 Classifications: {'peptide': 599} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 573} Restraints were copied for chains: B, C Time building chain proxies: 9.50, per 1000 atoms: 0.33 Number of scatterers: 29211 At special positions: 0 Unit cell: (107.06, 104.94, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 O 2712 8.00 N 2409 7.00 C 9369 6.00 H 14643 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 569 " distance=2.10 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 569 " distance=2.10 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 569 " distance=2.10 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: 2.02 Conformation dependent library (CDL) restraints added in 693.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 50.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 15 through 18 Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.648A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 61 through 82 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.320A pdb=" N VAL A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 362 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 removed outlier: 4.649A pdb=" N GLN A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 581 through 591 removed outlier: 4.964A pdb=" N PHE A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 15 through 18 Processing helix chain 'B' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.649A pdb=" N THR B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 53 through 60 Processing helix chain 'B' and resid 61 through 82 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN B 206 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 218 through 227 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.320A pdb=" N VAL B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 362 Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS B 384 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 529 removed outlier: 4.647A pdb=" N GLN B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 581 through 591 removed outlier: 4.963A pdb=" N PHE B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 15 through 18 Processing helix chain 'C' and resid 19 through 27 removed outlier: 3.532A pdb=" N VAL C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.648A pdb=" N THR C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 53 through 60 Processing helix chain 'C' and resid 61 through 82 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.832A pdb=" N ASN C 206 " --> pdb=" O GLN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 218 through 227 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.319A pdb=" N VAL C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 362 Processing helix chain 'C' and resid 378 through 384 removed outlier: 3.544A pdb=" N LYS C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 438 through 451 Processing helix chain 'C' and resid 470 through 481 removed outlier: 3.951A pdb=" N MET C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'C' and resid 488 through 505 removed outlier: 3.599A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 529 removed outlier: 4.648A pdb=" N GLN C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASP C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 581 through 591 removed outlier: 4.963A pdb=" N PHE C 587 " --> pdb=" O ASP C 583 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN A 279 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.611A pdb=" N ARG A 425 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 541 Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN B 279 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB4, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.612A pdb=" N ARG B 425 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB6, first strand: chain 'B' and resid 533 through 541 Processing sheet with id=AB7, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB8, first strand: chain 'C' and resid 275 through 276 removed outlier: 3.939A pdb=" N ASN C 279 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.611A pdb=" N ARG C 425 " --> pdb=" O LEU C 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AC3, first strand: chain 'C' and resid 533 through 541 666 hydrogen bonds defined for protein. 1845 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: 6.29 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 14631 1.13 - 1.31: 2707 1.31 - 1.49: 6372 1.49 - 1.67: 5672 1.67 - 1.85: 138 Bond restraints: 29520 Sorted by residual: bond pdb=" NH2 ARG A 211 " pdb="HH21 ARG A 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NH2 ARG B 211 " pdb="HH21 ARG B 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NE ARG A 201 " pdb=" HE ARG A 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" NH2 ARG C 211 " pdb="HH21 ARG C 211 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" NE ARG B 201 " pdb=" HE ARG B 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.56e+01 ... (remaining 29515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.93: 53085 10.93 - 21.87: 15 21.87 - 32.80: 75 32.80 - 43.73: 99 43.73 - 54.66: 87 Bond angle restraints: 53361 Sorted by residual: angle pdb=" C ASP B 309 " pdb=" N ILE B 310 " pdb=" CA ILE B 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP A 309 " pdb=" N ILE A 310 " pdb=" CA ILE A 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP C 309 " pdb=" N ILE C 310 " pdb=" CA ILE C 310 " ideal model delta sigma weight residual 122.59 147.12 -24.53 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C SER B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.37 157.42 -35.05 1.29e+00 6.01e-01 7.38e+02 angle pdb=" C SER C 6 " pdb=" N ILE C 7 " pdb=" CA ILE C 7 " ideal model delta sigma weight residual 122.37 157.41 -35.04 1.29e+00 6.01e-01 7.38e+02 ... (remaining 53356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 13374 17.28 - 34.55: 401 34.55 - 51.83: 139 51.83 - 69.11: 39 69.11 - 86.39: 6 Dihedral angle restraints: 13959 sinusoidal: 7584 harmonic: 6375 Sorted by residual: dihedral pdb=" C PHE C 474 " pdb=" N PHE C 474 " pdb=" CA PHE C 474 " pdb=" CB PHE C 474 " ideal model delta harmonic sigma weight residual -122.60 -113.90 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE A 474 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " pdb=" CB PHE A 474 " ideal model delta harmonic sigma weight residual -122.60 -113.92 -8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE B 474 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " pdb=" CB PHE B 474 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1156 0.064 - 0.129: 670 0.129 - 0.193: 323 0.193 - 0.257: 141 0.257 - 0.322: 23 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA PHE C 349 " pdb=" N PHE C 349 " pdb=" C PHE C 349 " pdb=" CB PHE C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE A 349 " pdb=" N PHE A 349 " pdb=" C PHE A 349 " pdb=" CB PHE A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHE B 349 " pdb=" N PHE B 349 " pdb=" C PHE B 349 " pdb=" CB PHE B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2310 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.31e+01 pdb=" CG TRP C 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP C 373 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP C 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP C 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP C 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP C 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP C 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP C 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP A 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 373 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP A 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP A 373 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP A 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP A 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP B 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 373 " -0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP B 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 373 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP B 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP B 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP B 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP B 373 " 0.043 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1719 2.13 - 2.75: 51445 2.75 - 3.37: 87024 3.37 - 3.98: 116701 3.98 - 4.60: 173952 Nonbonded interactions: 430841 Sorted by model distance: nonbonded pdb=" H THR B 137 " pdb=" HG1 THR B 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR C 137 " pdb=" HG1 THR C 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.515 2.100 nonbonded pdb=" H VAL C 182 " pdb=" HA VAL C 182 " model vdw 1.525 1.816 nonbonded pdb=" H VAL B 182 " pdb=" HA VAL B 182 " model vdw 1.525 1.816 ... (remaining 430836 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.170 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4235 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 : 0.020 0.176 14880 Z= 1.058 Angle : 2.624 35.398 20172 Z= 1.813 Chirality : 0.102 0.322 2313 Planarity : 0.010 0.054 2568 Dihedral : 9.975 86.385 5556 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 1791 helix: -1.52 (0.15), residues: 816 sheet: 2.08 (0.42), residues: 135 loop : 1.68 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 133 TYR 0.059 0.010 TYR C 173 PHE 0.040 0.006 PHE C 261 TRP 0.087 0.037 TRP A 373 HIS 0.022 0.003 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.02005 (14877) covalent geometry : angle 2.62424 (20166) SS BOND : bond 0.07168 ( 3) SS BOND : angle 2.31466 ( 6) hydrogen bonds : bond 0.19541 ( 666) hydrogen bonds : angle 7.53649 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7928 (tttt) cc_final: 0.7284 (tttm) REVERT: A 75 ASN cc_start: 0.7486 (m-40) cc_final: 0.7115 (m-40) REVERT: A 270 ASP cc_start: 0.7225 (t0) cc_final: 0.6498 (m-30) REVERT: B 41 LYS cc_start: 0.8089 (tttt) cc_final: 0.7428 (tttm) REVERT: B 75 ASN cc_start: 0.7415 (m-40) cc_final: 0.7150 (m-40) REVERT: B 270 ASP cc_start: 0.7179 (t0) cc_final: 0.6546 (m-30) REVERT: C 9 THR cc_start: 0.8251 (p) cc_final: 0.8031 (m) REVERT: C 41 LYS cc_start: 0.7978 (tttt) cc_final: 0.7691 (tttm) REVERT: C 270 ASP cc_start: 0.6936 (t0) cc_final: 0.6284 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2573 time to fit residues: 125.1752 Evaluate side-chains 278 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.287639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.237481 restraints weight = 51023.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.248267 restraints weight = 21978.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.255085 restraints weight = 13433.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.259160 restraints weight = 10064.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.261701 restraints weight = 8453.157| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14880 Z= 0.201 Angle : 1.134 21.321 20172 Z= 0.694 Chirality : 0.046 0.156 2313 Planarity : 0.005 0.049 2568 Dihedral : 5.016 24.421 1971 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1791 helix: -0.45 (0.16), residues: 828 sheet: 1.78 (0.45), residues: 129 loop : 1.25 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.022 0.002 TYR A 264 PHE 0.027 0.003 PHE B 352 TRP 0.024 0.004 TRP C 373 HIS 0.007 0.002 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00435 (14877) covalent geometry : angle 1.13352 (20166) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.26499 ( 6) hydrogen bonds : bond 0.06114 ( 666) hydrogen bonds : angle 5.66858 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.6829 (m-40) cc_final: 0.6414 (m-40) REVERT: B 75 ASN cc_start: 0.6946 (m-40) cc_final: 0.6524 (m-40) REVERT: B 260 MET cc_start: 0.5479 (mmt) cc_final: 0.5011 (mmp) REVERT: B 270 ASP cc_start: 0.6729 (t0) cc_final: 0.6203 (m-30) outliers start: 1 outliers final: 1 residues processed: 289 average time/residue: 0.2458 time to fit residues: 107.9176 Evaluate side-chains 274 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 518 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 39 GLN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.276133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.226116 restraints weight = 50165.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.235923 restraints weight = 22426.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.242030 restraints weight = 13960.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.245750 restraints weight = 10619.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.247862 restraints weight = 9003.795| |-----------------------------------------------------------------------------| r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14880 Z= 0.175 Angle : 1.083 22.330 20172 Z= 0.657 Chirality : 0.044 0.153 2313 Planarity : 0.004 0.058 2568 Dihedral : 4.796 23.906 1971 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.54 % Allowed : 6.14 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.20), residues: 1791 helix: -0.23 (0.17), residues: 801 sheet: 1.34 (0.46), residues: 129 loop : 0.90 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 140 TYR 0.023 0.002 TYR C 296 PHE 0.031 0.002 PHE B 477 TRP 0.022 0.004 TRP C 373 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00391 (14877) covalent geometry : angle 1.08321 (20166) SS BOND : bond 0.00511 ( 3) SS BOND : angle 0.85483 ( 6) hydrogen bonds : bond 0.04806 ( 666) hydrogen bonds : angle 5.35855 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 274 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 MET cc_start: 0.4720 (ttm) cc_final: 0.4492 (tpt) REVERT: A 260 MET cc_start: 0.6069 (mmp) cc_final: 0.5550 (mmt) REVERT: A 270 ASP cc_start: 0.6712 (t0) cc_final: 0.6257 (m-30) REVERT: B 75 ASN cc_start: 0.6964 (m-40) cc_final: 0.6629 (m-40) REVERT: B 270 ASP cc_start: 0.6823 (t0) cc_final: 0.6173 (m-30) REVERT: B 424 ILE cc_start: 0.7836 (mt) cc_final: 0.7016 (tp) REVERT: C 296 TYR cc_start: 0.6339 (m-80) cc_final: 0.5905 (m-80) outliers start: 9 outliers final: 6 residues processed: 279 average time/residue: 0.2278 time to fit residues: 96.0549 Evaluate side-chains 265 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 518 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 51 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.274574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.224433 restraints weight = 50183.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.233814 restraints weight = 22602.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.239819 restraints weight = 14217.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.243581 restraints weight = 10839.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.245497 restraints weight = 9185.217| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5044 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14880 Z= 0.161 Angle : 1.059 22.318 20172 Z= 0.642 Chirality : 0.044 0.150 2313 Planarity : 0.004 0.059 2568 Dihedral : 4.674 23.176 1971 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.84 % Allowed : 7.64 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1791 helix: -0.19 (0.17), residues: 798 sheet: 1.03 (0.47), residues: 129 loop : 0.66 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 140 TYR 0.015 0.002 TYR B 296 PHE 0.026 0.002 PHE B 290 TRP 0.021 0.004 TRP A 373 HIS 0.005 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00363 (14877) covalent geometry : angle 1.05881 (20166) SS BOND : bond 0.00556 ( 3) SS BOND : angle 0.95864 ( 6) hydrogen bonds : bond 0.04359 ( 666) hydrogen bonds : angle 5.17480 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 267 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.5981 (mmp) cc_final: 0.5504 (mmt) REVERT: B 97 ILE cc_start: 0.7915 (mt) cc_final: 0.7597 (mt) REVERT: B 270 ASP cc_start: 0.6875 (t0) cc_final: 0.6251 (m-30) REVERT: B 424 ILE cc_start: 0.7855 (mt) cc_final: 0.7139 (tp) REVERT: C 71 LYS cc_start: 0.5837 (tptt) cc_final: 0.5529 (tptt) REVERT: C 75 ASN cc_start: 0.6460 (m-40) cc_final: 0.6100 (m-40) REVERT: C 260 MET cc_start: 0.6358 (mmp) cc_final: 0.5864 (mmt) REVERT: C 270 ASP cc_start: 0.6551 (t0) cc_final: 0.6137 (m-30) outliers start: 14 outliers final: 11 residues processed: 277 average time/residue: 0.2375 time to fit residues: 101.0593 Evaluate side-chains 265 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.274725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.221818 restraints weight = 50449.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.231330 restraints weight = 22804.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.237253 restraints weight = 14496.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.240905 restraints weight = 11237.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.242925 restraints weight = 9676.205| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5174 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14880 Z= 0.195 Angle : 1.073 22.076 20172 Z= 0.649 Chirality : 0.045 0.158 2313 Planarity : 0.004 0.042 2568 Dihedral : 4.712 23.482 1971 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.20), residues: 1791 helix: -0.29 (0.18), residues: 798 sheet: 0.70 (0.49), residues: 129 loop : 0.46 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 425 TYR 0.016 0.002 TYR B 296 PHE 0.033 0.002 PHE B 290 TRP 0.014 0.003 TRP A 373 HIS 0.007 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00444 (14877) covalent geometry : angle 1.07251 (20166) SS BOND : bond 0.00533 ( 3) SS BOND : angle 1.20859 ( 6) hydrogen bonds : bond 0.04437 ( 666) hydrogen bonds : angle 5.25476 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6225 (mmp) cc_final: 0.5543 (mmt) REVERT: B 97 ILE cc_start: 0.7970 (mt) cc_final: 0.7707 (mt) REVERT: B 270 ASP cc_start: 0.6565 (t0) cc_final: 0.5910 (m-30) REVERT: C 71 LYS cc_start: 0.5909 (tptt) cc_final: 0.5622 (tptt) REVERT: C 75 ASN cc_start: 0.6467 (m-40) cc_final: 0.5952 (m-40) outliers start: 18 outliers final: 16 residues processed: 276 average time/residue: 0.2326 time to fit residues: 97.7385 Evaluate side-chains 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 172 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.273368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.221931 restraints weight = 49906.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.231239 restraints weight = 22663.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.237192 restraints weight = 14338.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.240863 restraints weight = 11014.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.242886 restraints weight = 9397.851| |-----------------------------------------------------------------------------| r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14880 Z= 0.142 Angle : 1.047 22.129 20172 Z= 0.635 Chirality : 0.043 0.166 2313 Planarity : 0.004 0.043 2568 Dihedral : 4.556 21.883 1971 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.08 % Allowed : 8.54 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1791 helix: -0.13 (0.18), residues: 798 sheet: 0.67 (0.49), residues: 129 loop : 0.56 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.024 0.001 TYR C 381 PHE 0.031 0.002 PHE B 290 TRP 0.011 0.002 TRP A 373 HIS 0.005 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00324 (14877) covalent geometry : angle 1.04563 (20166) SS BOND : bond 0.00674 ( 3) SS BOND : angle 3.43492 ( 6) hydrogen bonds : bond 0.03910 ( 666) hydrogen bonds : angle 5.02267 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6206 (mmp) cc_final: 0.5508 (mmt) REVERT: B 97 ILE cc_start: 0.8020 (mt) cc_final: 0.7766 (mt) REVERT: B 270 ASP cc_start: 0.6526 (t0) cc_final: 0.5919 (m-30) REVERT: C 71 LYS cc_start: 0.5711 (tptt) cc_final: 0.5442 (tptt) REVERT: C 75 ASN cc_start: 0.6532 (m-40) cc_final: 0.6053 (m-40) outliers start: 18 outliers final: 17 residues processed: 269 average time/residue: 0.2350 time to fit residues: 96.1409 Evaluate side-chains 273 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 315 ASN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.268552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.214191 restraints weight = 51374.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.223670 restraints weight = 23757.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.229652 restraints weight = 15225.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.233214 restraints weight = 11812.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.235574 restraints weight = 10161.799| |-----------------------------------------------------------------------------| r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5270 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14880 Z= 0.227 Angle : 1.092 22.002 20172 Z= 0.657 Chirality : 0.045 0.187 2313 Planarity : 0.005 0.047 2568 Dihedral : 4.827 32.729 1971 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.38 % Allowed : 9.99 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1791 helix: -0.37 (0.18), residues: 798 sheet: 0.53 (0.49), residues: 129 loop : 0.08 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 140 TYR 0.025 0.002 TYR C 381 PHE 0.035 0.003 PHE B 352 TRP 0.009 0.002 TRP A 373 HIS 0.009 0.002 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00517 (14877) covalent geometry : angle 1.09202 (20166) SS BOND : bond 0.02024 ( 3) SS BOND : angle 1.12307 ( 6) hydrogen bonds : bond 0.04472 ( 666) hydrogen bonds : angle 5.30129 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 265 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.7725 (m) cc_final: 0.7111 (p) REVERT: A 260 MET cc_start: 0.6276 (mmp) cc_final: 0.5571 (mmt) REVERT: B 31 CYS cc_start: 0.1821 (OUTLIER) cc_final: 0.1011 (m) REVERT: B 87 LEU cc_start: 0.7524 (mt) cc_final: 0.7252 (mt) REVERT: B 97 ILE cc_start: 0.8036 (mt) cc_final: 0.7807 (mt) REVERT: B 270 ASP cc_start: 0.6322 (t0) cc_final: 0.5742 (m-30) REVERT: C 71 LYS cc_start: 0.6040 (tptt) cc_final: 0.5755 (tptt) REVERT: C 75 ASN cc_start: 0.6607 (m-40) cc_final: 0.6000 (m-40) outliers start: 23 outliers final: 20 residues processed: 276 average time/residue: 0.2255 time to fit residues: 95.1733 Evaluate side-chains 278 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 31 CYS Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 24 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.272481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.223134 restraints weight = 49755.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.232525 restraints weight = 22276.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.238280 restraints weight = 13844.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.241953 restraints weight = 10533.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.243988 restraints weight = 8915.255| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5156 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14880 Z= 0.138 Angle : 1.055 22.240 20172 Z= 0.637 Chirality : 0.044 0.194 2313 Planarity : 0.004 0.045 2568 Dihedral : 4.608 26.751 1971 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.20 % Allowed : 10.65 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.20), residues: 1791 helix: -0.17 (0.18), residues: 798 sheet: 0.69 (0.50), residues: 129 loop : 0.22 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.026 0.001 TYR A 381 PHE 0.033 0.002 PHE B 290 TRP 0.009 0.002 TRP A 373 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00316 (14877) covalent geometry : angle 1.05501 (20166) SS BOND : bond 0.00376 ( 3) SS BOND : angle 1.85939 ( 6) hydrogen bonds : bond 0.03859 ( 666) hydrogen bonds : angle 5.01736 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6250 (mmp) cc_final: 0.5603 (mmt) REVERT: B 97 ILE cc_start: 0.8014 (mt) cc_final: 0.7784 (mt) REVERT: B 270 ASP cc_start: 0.6375 (t0) cc_final: 0.5766 (m-30) REVERT: B 374 ASP cc_start: 0.8211 (m-30) cc_final: 0.7970 (m-30) REVERT: B 541 MET cc_start: 0.0555 (ttp) cc_final: 0.0037 (ttp) REVERT: C 71 LYS cc_start: 0.5784 (tptt) cc_final: 0.5436 (tptt) REVERT: C 75 ASN cc_start: 0.6496 (m-40) cc_final: 0.5869 (m-40) REVERT: C 91 THR cc_start: 0.7824 (m) cc_final: 0.7066 (p) outliers start: 20 outliers final: 19 residues processed: 272 average time/residue: 0.2263 time to fit residues: 93.6055 Evaluate side-chains 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.269601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.215714 restraints weight = 51189.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.225294 restraints weight = 23432.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.231326 restraints weight = 14932.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.234978 restraints weight = 11559.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.236890 restraints weight = 9933.658| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14880 Z= 0.174 Angle : 1.070 22.150 20172 Z= 0.644 Chirality : 0.044 0.193 2313 Planarity : 0.004 0.046 2568 Dihedral : 4.660 30.665 1971 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.14 % Allowed : 10.95 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1791 helix: -0.19 (0.18), residues: 795 sheet: 0.72 (0.50), residues: 129 loop : 0.04 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.025 0.002 TYR A 381 PHE 0.035 0.002 PHE B 477 TRP 0.008 0.002 TRP C 373 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00402 (14877) covalent geometry : angle 1.07040 (20166) SS BOND : bond 0.00325 ( 3) SS BOND : angle 1.32568 ( 6) hydrogen bonds : bond 0.04091 ( 666) hydrogen bonds : angle 5.09284 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6159 (mmp) cc_final: 0.5560 (mmt) REVERT: A 374 ASP cc_start: 0.8213 (m-30) cc_final: 0.8006 (m-30) REVERT: B 97 ILE cc_start: 0.8159 (mt) cc_final: 0.7927 (mt) REVERT: B 270 ASP cc_start: 0.6432 (t0) cc_final: 0.5788 (m-30) REVERT: B 347 LYS cc_start: 0.6766 (mttp) cc_final: 0.6386 (ttpp) REVERT: B 374 ASP cc_start: 0.8378 (m-30) cc_final: 0.7957 (m-30) REVERT: B 541 MET cc_start: 0.0506 (ttp) cc_final: 0.0024 (ttp) REVERT: C 71 LYS cc_start: 0.5789 (tptt) cc_final: 0.5431 (tptt) REVERT: C 75 ASN cc_start: 0.6462 (m-40) cc_final: 0.5781 (m-40) outliers start: 19 outliers final: 18 residues processed: 274 average time/residue: 0.2224 time to fit residues: 93.8864 Evaluate side-chains 271 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 125 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.269515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.216599 restraints weight = 50873.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.226066 restraints weight = 23606.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.232015 restraints weight = 15134.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.235532 restraints weight = 11714.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.237643 restraints weight = 10088.307| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5251 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14880 Z= 0.164 Angle : 1.067 22.109 20172 Z= 0.642 Chirality : 0.044 0.194 2313 Planarity : 0.004 0.048 2568 Dihedral : 4.650 30.203 1971 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.14 % Allowed : 11.31 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1791 helix: -0.19 (0.18), residues: 795 sheet: 0.80 (0.50), residues: 129 loop : 0.01 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.029 0.002 TYR A 381 PHE 0.042 0.002 PHE A 290 TRP 0.009 0.002 TRP C 373 HIS 0.006 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00378 (14877) covalent geometry : angle 1.06688 (20166) SS BOND : bond 0.00413 ( 3) SS BOND : angle 1.62390 ( 6) hydrogen bonds : bond 0.04021 ( 666) hydrogen bonds : angle 5.05396 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6143 (mmp) cc_final: 0.5396 (mmt) REVERT: A 316 ILE cc_start: 0.5372 (tp) cc_final: 0.5110 (tp) REVERT: A 374 ASP cc_start: 0.8308 (m-30) cc_final: 0.8089 (m-30) REVERT: B 97 ILE cc_start: 0.8106 (mt) cc_final: 0.7873 (mt) REVERT: B 270 ASP cc_start: 0.6349 (t0) cc_final: 0.5670 (m-30) REVERT: B 347 LYS cc_start: 0.6827 (mttp) cc_final: 0.6596 (ttpt) REVERT: B 374 ASP cc_start: 0.8440 (m-30) cc_final: 0.7999 (m-30) REVERT: B 381 TYR cc_start: 0.6420 (t80) cc_final: 0.4093 (t80) REVERT: B 541 MET cc_start: 0.0508 (ttp) cc_final: 0.0033 (ttp) REVERT: C 71 LYS cc_start: 0.5704 (tptt) cc_final: 0.5460 (tptt) outliers start: 19 outliers final: 17 residues processed: 269 average time/residue: 0.2201 time to fit residues: 89.5336 Evaluate side-chains 271 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 512 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.0270 chunk 40 optimal weight: 0.3980 chunk 172 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.282989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.231720 restraints weight = 51286.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.241884 restraints weight = 23009.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.248116 restraints weight = 14480.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.251978 restraints weight = 11127.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.254308 restraints weight = 9462.468| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5177 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14880 Z= 0.124 Angle : 1.053 22.311 20172 Z= 0.634 Chirality : 0.043 0.190 2313 Planarity : 0.004 0.048 2568 Dihedral : 4.512 28.517 1971 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.02 % Allowed : 11.67 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.21), residues: 1791 helix: 0.03 (0.19), residues: 774 sheet: 0.84 (0.49), residues: 129 loop : 0.22 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.027 0.001 TYR A 381 PHE 0.039 0.002 PHE B 477 TRP 0.010 0.003 TRP C 373 HIS 0.005 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00286 (14877) covalent geometry : angle 1.05238 (20166) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.42136 ( 6) hydrogen bonds : bond 0.03691 ( 666) hydrogen bonds : angle 4.89009 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.25 seconds wall clock time: 78 minutes 11.95 seconds (4691.95 seconds total)