Starting phenix.real_space_refine on Tue May 27 08:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4k_17410/05_2025/8p4k_17410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4k_17410/05_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_17410/05_2025/8p4k_17410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4k_17410/05_2025/8p4k_17410.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4k_17410/05_2025/8p4k_17410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4k_17410/05_2025/8p4k_17410.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.205 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B Time building chain proxies: 27.79, per 1000 atoms: 0.95 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 C 31 " - pdb=" SG CYS C 569 " distance=2.10 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 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: 7.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.24 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: 10.48 Time building geometry restraints manager: 8.54 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.490 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 71.860 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.650 ------------------------------------------------------------------------------- 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 : 1.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), 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 TRP 0.087 0.037 TRP A 373 HIS 0.022 0.003 HIS A 117 PHE 0.040 0.006 PHE C 261 TYR 0.059 0.010 TYR C 173 ARG 0.013 0.001 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.19541 ( 666) hydrogen bonds : angle 7.53649 ( 1845) SS BOND : bond 0.07168 ( 3) SS BOND : angle 2.31466 ( 6) covalent geometry : bond 0.02005 (14877) covalent geometry : angle 2.62424 (20166) *********************** 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 : 1.996 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: 0.5950 time to fit residues: 286.3014 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 : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4858 r_free = 0.4858 target = 0.280253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.229217 restraints weight = 50648.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.239450 restraints weight = 22450.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.245998 restraints weight = 13940.445| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4964 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14880 Z= 0.197 Angle : 1.116 21.047 20172 Z= 0.680 Chirality : 0.046 0.148 2313 Planarity : 0.005 0.052 2568 Dihedral : 5.098 24.680 1971 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.06 % Allowed : 5.17 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1791 helix: -0.39 (0.17), residues: 810 sheet: 1.78 (0.47), residues: 123 loop : 1.17 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 373 HIS 0.006 0.002 HIS A 128 PHE 0.024 0.003 PHE C 348 TYR 0.022 0.002 TYR A 264 ARG 0.004 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.05795 ( 666) hydrogen bonds : angle 5.66878 ( 1845) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.20640 ( 6) covalent geometry : bond 0.00433 (14877) covalent geometry : angle 1.11581 (20166) *********************** 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 291 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 2.013 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: A 75 ASN cc_start: 0.6817 (m-40) cc_final: 0.6406 (m-40) REVERT: B 75 ASN cc_start: 0.6915 (m-40) cc_final: 0.6478 (m-40) REVERT: B 260 MET cc_start: 0.5480 (mmt) cc_final: 0.5022 (mmp) REVERT: B 270 ASP cc_start: 0.6813 (t0) cc_final: 0.6245 (m-30) REVERT: C 55 SER cc_start: 0.8691 (p) cc_final: 0.8395 (t) REVERT: C 290 PHE cc_start: 0.5781 (t80) cc_final: 0.5429 (t80) outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.5643 time to fit residues: 245.1570 Evaluate side-chains 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 122 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.271658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.220645 restraints weight = 50399.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.230059 restraints weight = 22901.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.235852 restraints weight = 14510.260| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5198 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14880 Z= 0.229 Angle : 1.121 22.360 20172 Z= 0.676 Chirality : 0.045 0.163 2313 Planarity : 0.005 0.062 2568 Dihedral : 4.951 24.870 1971 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.72 % Allowed : 6.14 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1791 helix: -0.46 (0.17), residues: 801 sheet: 0.93 (0.48), residues: 129 loop : 0.50 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP C 373 HIS 0.007 0.002 HIS C 319 PHE 0.033 0.002 PHE B 477 TYR 0.033 0.002 TYR B 296 ARG 0.004 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.05148 ( 666) hydrogen bonds : angle 5.55804 ( 1845) SS BOND : bond 0.00718 ( 3) SS BOND : angle 1.04162 ( 6) covalent geometry : bond 0.00513 (14877) covalent geometry : angle 1.12072 (20166) *********************** 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 289 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 277 time to evaluate : 2.101 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: A 97 ILE cc_start: 0.7889 (mt) cc_final: 0.7656 (mt) REVERT: A 260 MET cc_start: 0.5902 (mmp) cc_final: 0.5489 (mmt) REVERT: B 97 ILE cc_start: 0.7936 (mt) cc_final: 0.7607 (mt) REVERT: B 270 ASP cc_start: 0.6759 (t0) cc_final: 0.6038 (m-30) REVERT: B 424 ILE cc_start: 0.7986 (mt) cc_final: 0.7143 (tp) REVERT: C 55 SER cc_start: 0.8685 (p) cc_final: 0.8440 (t) REVERT: C 71 LYS cc_start: 0.6024 (tptt) cc_final: 0.5793 (tptt) REVERT: C 75 ASN cc_start: 0.6490 (m-40) cc_final: 0.6216 (m-40) REVERT: C 270 ASP cc_start: 0.6580 (t0) cc_final: 0.6094 (m-30) REVERT: C 296 TYR cc_start: 0.6251 (m-80) cc_final: 0.5865 (m-80) outliers start: 12 outliers final: 9 residues processed: 283 average time/residue: 0.5529 time to fit residues: 235.8320 Evaluate side-chains 267 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain B residue 66 GLN 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 C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 155 optimal weight: 0.0000 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 = 0.4793 r_free = 0.4793 target = 0.272505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.221881 restraints weight = 50465.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.231211 restraints weight = 22698.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.237134 restraints weight = 14239.226| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5160 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14880 Z= 0.163 Angle : 1.056 22.023 20172 Z= 0.641 Chirality : 0.044 0.155 2313 Planarity : 0.004 0.041 2568 Dihedral : 4.761 23.888 1971 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.66 % Allowed : 7.28 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1791 helix: -0.35 (0.17), residues: 801 sheet: 0.71 (0.49), residues: 129 loop : 0.42 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 373 HIS 0.006 0.001 HIS B 117 PHE 0.024 0.002 PHE B 352 TYR 0.016 0.001 TYR B 296 ARG 0.003 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 666) hydrogen bonds : angle 5.22427 ( 1845) SS BOND : bond 0.00545 ( 3) SS BOND : angle 1.49708 ( 6) covalent geometry : bond 0.00367 (14877) covalent geometry : angle 1.05556 (20166) *********************** 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 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 2.101 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: 0.5549 (mmt) REVERT: B 97 ILE cc_start: 0.7978 (mt) cc_final: 0.7716 (mt) REVERT: B 270 ASP cc_start: 0.6593 (t0) cc_final: 0.5910 (m-30) REVERT: B 347 LYS cc_start: 0.6688 (mttp) cc_final: 0.6352 (ttpp) REVERT: C 71 LYS cc_start: 0.5912 (tptt) cc_final: 0.5605 (tptt) REVERT: C 75 ASN cc_start: 0.6568 (m-40) cc_final: 0.6195 (m-40) REVERT: C 260 MET cc_start: 0.6328 (mmp) cc_final: 0.5835 (mmt) outliers start: 11 outliers final: 9 residues processed: 273 average time/residue: 0.5588 time to fit residues: 229.1853 Evaluate side-chains 265 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 256 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE 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 137 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 149 optimal weight: 0.3980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4804 r_free = 0.4804 target = 0.273678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.222781 restraints weight = 50161.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.232280 restraints weight = 22691.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.238255 restraints weight = 14316.124| |-----------------------------------------------------------------------------| r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5152 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14880 Z= 0.132 Angle : 1.042 22.278 20172 Z= 0.633 Chirality : 0.043 0.149 2313 Planarity : 0.004 0.041 2568 Dihedral : 4.546 22.446 1971 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.78 % Allowed : 8.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1791 helix: -0.11 (0.18), residues: 798 sheet: 0.67 (0.48), residues: 129 loop : 0.63 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 373 HIS 0.004 0.001 HIS C 128 PHE 0.033 0.002 PHE C 477 TYR 0.011 0.001 TYR B 500 ARG 0.002 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 666) hydrogen bonds : angle 5.00567 ( 1845) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.21242 ( 6) covalent geometry : bond 0.00302 (14877) covalent geometry : angle 1.04153 (20166) *********************** 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 272 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 2.232 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: 0.6204 (mmp) cc_final: 0.5589 (mmt) REVERT: B 97 ILE cc_start: 0.7999 (mt) cc_final: 0.7741 (mt) REVERT: B 270 ASP cc_start: 0.6600 (t0) cc_final: 0.5947 (m-30) REVERT: B 347 LYS cc_start: 0.6645 (mttp) cc_final: 0.6319 (ttpp) REVERT: C 71 LYS cc_start: 0.5671 (tptt) cc_final: 0.5381 (tptt) REVERT: C 75 ASN cc_start: 0.6571 (m-40) cc_final: 0.6045 (m-40) REVERT: C 389 MET cc_start: 0.5529 (ttm) cc_final: 0.5130 (ttm) outliers start: 13 outliers final: 12 residues processed: 267 average time/residue: 0.5497 time to fit residues: 218.9511 Evaluate side-chains 268 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 584 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 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 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 124 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 138 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN C 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.275007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.222211 restraints weight = 50592.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.232035 restraints weight = 22933.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.238231 restraints weight = 14467.882| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5238 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14880 Z= 0.162 Angle : 1.055 22.197 20172 Z= 0.639 Chirality : 0.043 0.165 2313 Planarity : 0.004 0.042 2568 Dihedral : 4.583 22.099 1971 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.14 % Allowed : 8.90 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1791 helix: -0.16 (0.18), residues: 798 sheet: 0.62 (0.49), residues: 129 loop : 0.45 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 373 HIS 0.005 0.001 HIS A 128 PHE 0.030 0.002 PHE B 290 TYR 0.021 0.002 TYR C 381 ARG 0.003 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 666) hydrogen bonds : angle 5.05488 ( 1845) SS BOND : bond 0.00439 ( 3) SS BOND : angle 3.09602 ( 6) covalent geometry : bond 0.00372 (14877) covalent geometry : angle 1.05400 (20166) *********************** 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 280 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 2.434 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 260 MET cc_start: 0.6228 (mmp) cc_final: 0.5534 (mmt) REVERT: B 91 THR cc_start: 0.7780 (m) cc_final: 0.7099 (p) REVERT: B 97 ILE cc_start: 0.7942 (mt) cc_final: 0.7725 (mt) REVERT: B 270 ASP cc_start: 0.6587 (t0) cc_final: 0.5912 (m-30) REVERT: C 66 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: C 71 LYS cc_start: 0.5716 (tptt) cc_final: 0.5467 (tptt) REVERT: C 75 ASN cc_start: 0.6513 (m-40) cc_final: 0.5952 (m-40) REVERT: C 389 MET cc_start: 0.5350 (ttm) cc_final: 0.5131 (ttm) outliers start: 19 outliers final: 17 residues processed: 271 average time/residue: 0.5413 time to fit residues: 220.8656 Evaluate side-chains 273 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 584 LEU Chi-restraints excluded: chain B residue 66 GLN 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 66 GLN Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 465 MET 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 21 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.272485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.220617 restraints weight = 50222.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.229957 restraints weight = 23112.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.235924 restraints weight = 14711.115| |-----------------------------------------------------------------------------| r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5232 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14880 Z= 0.151 Angle : 1.056 22.319 20172 Z= 0.638 Chirality : 0.043 0.177 2313 Planarity : 0.004 0.043 2568 Dihedral : 4.578 29.536 1971 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.20 % Allowed : 9.57 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1791 helix: -0.13 (0.18), residues: 795 sheet: 0.63 (0.49), residues: 129 loop : 0.33 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.008 0.001 HIS B 117 PHE 0.033 0.002 PHE C 477 TYR 0.026 0.001 TYR C 381 ARG 0.002 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 666) hydrogen bonds : angle 5.02946 ( 1845) SS BOND : bond 0.00721 ( 3) SS BOND : angle 1.94022 ( 6) covalent geometry : bond 0.00347 (14877) covalent geometry : angle 1.05562 (20166) *********************** 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 274 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 2.016 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: A 260 MET cc_start: 0.6161 (mmp) cc_final: 0.5505 (mmt) REVERT: B 91 THR cc_start: 0.7709 (m) cc_final: 0.6883 (p) REVERT: B 97 ILE cc_start: 0.7988 (mt) cc_final: 0.7758 (mt) REVERT: B 270 ASP cc_start: 0.6510 (t0) cc_final: 0.5845 (m-30) REVERT: C 66 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6934 (mp10) REVERT: C 71 LYS cc_start: 0.5878 (tptt) cc_final: 0.5556 (tptt) REVERT: C 75 ASN cc_start: 0.6533 (m-40) cc_final: 0.5977 (m-40) outliers start: 20 outliers final: 17 residues processed: 267 average time/residue: 0.5450 time to fit residues: 220.4524 Evaluate side-chains 273 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 66 GLN 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 66 GLN Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 500 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 172 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 148 optimal weight: 0.4980 chunk 10 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 = 0.4802 r_free = 0.4802 target = 0.273790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.223650 restraints weight = 50015.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.232903 restraints weight = 22472.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.238866 restraints weight = 14189.457| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5195 moved from start: 0.4649 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= 0.129 Angle : 1.048 22.366 20172 Z= 0.633 Chirality : 0.043 0.184 2313 Planarity : 0.004 0.044 2568 Dihedral : 4.486 31.740 1971 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.02 % Allowed : 10.41 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1791 helix: -0.05 (0.18), residues: 795 sheet: 0.68 (0.49), residues: 129 loop : 0.37 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 373 HIS 0.007 0.001 HIS B 117 PHE 0.041 0.002 PHE A 290 TYR 0.023 0.001 TYR C 381 ARG 0.002 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 666) hydrogen bonds : angle 4.95055 ( 1845) SS BOND : bond 0.00454 ( 3) SS BOND : angle 1.59315 ( 6) covalent geometry : bond 0.00296 (14877) covalent geometry : angle 1.04780 (20166) *********************** 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 276 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 259 time to evaluate : 2.238 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 260 MET cc_start: 0.6202 (mmp) cc_final: 0.5576 (mmt) REVERT: B 91 THR cc_start: 0.7674 (m) cc_final: 0.6847 (p) REVERT: B 97 ILE cc_start: 0.8176 (mt) cc_final: 0.7971 (mt) REVERT: B 270 ASP cc_start: 0.6457 (t0) cc_final: 0.5813 (m-30) REVERT: B 541 MET cc_start: 0.0536 (ttp) cc_final: 0.0018 (ttp) REVERT: C 71 LYS cc_start: 0.5708 (tptt) cc_final: 0.5469 (tptt) outliers start: 17 outliers final: 16 residues processed: 270 average time/residue: 0.5419 time to fit residues: 221.1099 Evaluate side-chains 271 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 66 GLN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 465 MET 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 128 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4777 r_free = 0.4777 target = 0.270831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.217006 restraints weight = 51528.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.226906 restraints weight = 23512.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.232904 restraints weight = 14847.906| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5274 moved from start: 0.4876 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= 0.160 Angle : 1.060 22.295 20172 Z= 0.640 Chirality : 0.044 0.187 2313 Planarity : 0.004 0.045 2568 Dihedral : 4.544 31.138 1971 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.90 % Allowed : 10.95 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1791 helix: -0.07 (0.19), residues: 795 sheet: 0.80 (0.50), residues: 129 loop : 0.23 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.007 0.001 HIS B 117 PHE 0.037 0.002 PHE A 290 TYR 0.021 0.002 TYR C 381 ARG 0.004 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 666) hydrogen bonds : angle 5.00302 ( 1845) SS BOND : bond 0.00454 ( 3) SS BOND : angle 1.65250 ( 6) covalent geometry : bond 0.00364 (14877) covalent geometry : angle 1.05968 (20166) *********************** 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 275 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 2.297 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: 0.6186 (mmp) cc_final: 0.5577 (mmt) REVERT: B 91 THR cc_start: 0.7738 (m) cc_final: 0.6904 (p) REVERT: B 97 ILE cc_start: 0.8068 (mt) cc_final: 0.7857 (mt) REVERT: B 270 ASP cc_start: 0.6494 (t0) cc_final: 0.5822 (m-30) REVERT: B 541 MET cc_start: 0.0491 (ttp) cc_final: 0.0005 (ttp) REVERT: C 71 LYS cc_start: 0.5825 (tptt) cc_final: 0.5450 (tptt) REVERT: C 75 ASN cc_start: 0.6542 (m-40) cc_final: 0.5889 (m-40) outliers start: 15 outliers final: 15 residues processed: 270 average time/residue: 0.5524 time to fit residues: 225.6347 Evaluate side-chains 268 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 253 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 66 GLN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU 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 40 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 176 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.270789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.222296 restraints weight = 49677.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.231205 restraints weight = 23128.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.236789 restraints weight = 14680.860| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14880 Z= 0.137 Angle : 1.050 22.350 20172 Z= 0.634 Chirality : 0.043 0.185 2313 Planarity : 0.004 0.046 2568 Dihedral : 4.477 29.496 1971 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.02 % Allowed : 11.43 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1791 helix: -0.01 (0.19), residues: 795 sheet: 0.82 (0.50), residues: 129 loop : 0.22 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 373 HIS 0.006 0.001 HIS B 117 PHE 0.035 0.002 PHE B 477 TYR 0.022 0.001 TYR C 381 ARG 0.003 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 666) hydrogen bonds : angle 4.91821 ( 1845) SS BOND : bond 0.00392 ( 3) SS BOND : angle 1.50179 ( 6) covalent geometry : bond 0.00313 (14877) covalent geometry : angle 1.04940 (20166) ********************** 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 271 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 2.071 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: 0.6113 (mmp) cc_final: 0.5370 (mmt) REVERT: B 91 THR cc_start: 0.7747 (m) cc_final: 0.6910 (p) REVERT: B 97 ILE cc_start: 0.8084 (mt) cc_final: 0.7865 (mt) REVERT: B 270 ASP cc_start: 0.6358 (t0) cc_final: 0.5735 (m-30) REVERT: B 541 MET cc_start: 0.0485 (ttp) cc_final: 0.0004 (ttp) REVERT: C 71 LYS cc_start: 0.5720 (tptt) cc_final: 0.5332 (tptt) REVERT: C 75 ASN cc_start: 0.6496 (m-40) cc_final: 0.5821 (m-40) outliers start: 17 outliers final: 16 residues processed: 265 average time/residue: 0.5534 time to fit residues: 222.4793 Evaluate side-chains 267 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER 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 66 GLN Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU 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 38 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.269987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.217033 restraints weight = 51171.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.226493 restraints weight = 23811.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.232454 restraints weight = 15251.559| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14880 Z= 0.160 Angle : 1.057 22.203 20172 Z= 0.638 Chirality : 0.044 0.188 2313 Planarity : 0.004 0.048 2568 Dihedral : 4.537 28.552 1971 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.02 % Allowed : 11.31 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1791 helix: -0.12 (0.19), residues: 795 sheet: 0.82 (0.49), residues: 129 loop : 0.10 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.006 0.001 HIS B 117 PHE 0.036 0.002 PHE B 477 TYR 0.018 0.001 TYR C 381 ARG 0.003 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 666) hydrogen bonds : angle 5.01113 ( 1845) SS BOND : bond 0.00432 ( 3) SS BOND : angle 1.54411 ( 6) covalent geometry : bond 0.00366 (14877) covalent geometry : angle 1.05694 (20166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9133.10 seconds wall clock time: 158 minutes 29.02 seconds (9509.02 seconds total)