Starting phenix.real_space_refine on Wed Jun 25 07:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4k_17410/06_2025/8p4k_17410.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4k_17410/06_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_17410/06_2025/8p4k_17410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4k_17410/06_2025/8p4k_17410.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4k_17410/06_2025/8p4k_17410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4k_17410/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 29.10, per 1000 atoms: 1.00 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: 8.07 Conformation dependent library (CDL) restraints added in 2.5 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: 2.63 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: 12.52 Time building geometry restraints manager: 9.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 14631 1.13 - 1.31: 2707 1.31 - 1.49: 6372 1.49 - 1.67: 5672 1.67 - 1.85: 138 Bond restraints: 29520 Sorted by residual: bond pdb=" NH2 ARG A 211 " pdb="HH21 ARG A 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NH2 ARG B 211 " pdb="HH21 ARG B 211 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NE ARG A 201 " pdb=" HE ARG A 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" NH2 ARG C 211 " pdb="HH21 ARG C 211 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.57e+01 bond pdb=" NE ARG B 201 " pdb=" HE ARG B 201 " ideal model delta sigma weight residual 0.860 1.045 -0.185 2.00e-02 2.50e+03 8.56e+01 ... (remaining 29515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.93: 53085 10.93 - 21.87: 15 21.87 - 32.80: 75 32.80 - 43.73: 99 43.73 - 54.66: 87 Bond angle restraints: 53361 Sorted by residual: angle pdb=" C ASP B 309 " pdb=" N ILE B 310 " pdb=" CA ILE B 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP A 309 " pdb=" N ILE A 310 " pdb=" CA ILE A 310 " ideal model delta sigma weight residual 122.59 147.14 -24.55 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C ASP C 309 " pdb=" N ILE C 310 " pdb=" CA ILE C 310 " ideal model delta sigma weight residual 122.59 147.12 -24.53 7.20e-01 1.93e+00 1.16e+03 angle pdb=" C SER B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.37 157.42 -35.05 1.29e+00 6.01e-01 7.38e+02 angle pdb=" C SER C 6 " pdb=" N ILE C 7 " pdb=" CA ILE C 7 " ideal model delta sigma weight residual 122.37 157.41 -35.04 1.29e+00 6.01e-01 7.38e+02 ... (remaining 53356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 13374 17.28 - 34.55: 401 34.55 - 51.83: 139 51.83 - 69.11: 39 69.11 - 86.39: 6 Dihedral angle restraints: 13959 sinusoidal: 7584 harmonic: 6375 Sorted by residual: dihedral pdb=" C PHE C 474 " pdb=" N PHE C 474 " pdb=" CA PHE C 474 " pdb=" CB PHE C 474 " ideal model delta harmonic sigma weight residual -122.60 -113.90 -8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE A 474 " pdb=" N PHE A 474 " pdb=" CA PHE A 474 " pdb=" CB PHE A 474 " ideal model delta harmonic sigma weight residual -122.60 -113.92 -8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" C PHE B 474 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " pdb=" CB PHE B 474 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1156 0.064 - 0.129: 670 0.129 - 0.193: 323 0.193 - 0.257: 141 0.257 - 0.322: 23 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA PHE C 349 " pdb=" N PHE C 349 " pdb=" C PHE C 349 " pdb=" CB PHE C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE A 349 " pdb=" N PHE A 349 " pdb=" C PHE A 349 " pdb=" CB PHE A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHE B 349 " pdb=" N PHE B 349 " pdb=" C PHE B 349 " pdb=" CB PHE B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2310 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.31e+01 pdb=" CG TRP C 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP C 373 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP C 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP C 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP C 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP C 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP C 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP C 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP A 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 373 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 373 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP A 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 373 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP A 373 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP A 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP A 373 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 373 " 0.139 2.00e-02 2.50e+03 4.82e-02 9.30e+01 pdb=" CG TRP B 373 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP B 373 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 373 " -0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP B 373 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP B 373 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 373 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 373 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP B 373 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP B 373 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TRP B 373 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP B 373 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 373 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 373 " -0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP B 373 " 0.043 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1719 2.13 - 2.75: 51445 2.75 - 3.37: 87024 3.37 - 3.98: 116701 3.98 - 4.60: 173952 Nonbonded interactions: 430841 Sorted by model distance: nonbonded pdb=" H THR B 137 " pdb=" HG1 THR B 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR C 137 " pdb=" HG1 THR C 137 " model vdw 1.515 2.100 nonbonded pdb=" H THR A 137 " pdb=" HG1 THR A 137 " model vdw 1.515 2.100 nonbonded pdb=" H VAL C 182 " pdb=" HA VAL C 182 " model vdw 1.525 1.816 nonbonded pdb=" H VAL B 182 " pdb=" HA VAL B 182 " model vdw 1.525 1.816 ... (remaining 430836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.470 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 80.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.340 ------------------------------------------------------------------------------- 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 : 2.155 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: 0.6129 time to fit residues: 296.2226 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 : 2.177 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.229137 restraints weight = 50648.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.239455 restraints weight = 22481.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.245960 restraints weight = 13950.877| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 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 : 5.240 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: 0.6811 (m-40) cc_final: 0.6402 (m-40) REVERT: B 75 ASN cc_start: 0.6910 (m-40) cc_final: 0.6474 (m-40) REVERT: B 260 MET cc_start: 0.5484 (mmt) cc_final: 0.5025 (mmp) REVERT: B 270 ASP cc_start: 0.6815 (t0) cc_final: 0.6246 (m-30) REVERT: C 55 SER cc_start: 0.8689 (p) cc_final: 0.8393 (t) REVERT: C 290 PHE cc_start: 0.5780 (t80) cc_final: 0.5428 (t80) outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.7331 time to fit residues: 323.3786 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 : 2.324 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 0.9990 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: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.272059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.221167 restraints weight = 50439.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.230576 restraints weight = 23011.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.236418 restraints weight = 14627.206| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5200 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 14880 Z= 0.231 Angle : 1.125 22.329 20172 Z= 0.678 Chirality : 0.045 0.164 2313 Planarity : 0.005 0.063 2568 Dihedral : 4.971 24.923 1971 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.72 % Allowed : 6.26 % Favored : 93.02 % 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 (0.20), residues: 1791 helix: -0.50 (0.17), residues: 801 sheet: 0.89 (0.48), residues: 129 loop : 0.45 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 373 HIS 0.007 0.002 HIS C 319 PHE 0.034 0.003 PHE B 477 TYR 0.036 0.002 TYR B 296 ARG 0.004 0.001 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 666) hydrogen bonds : angle 5.57032 ( 1845) SS BOND : bond 0.00742 ( 3) SS BOND : angle 1.02777 ( 6) covalent geometry : bond 0.00519 (14877) covalent geometry : angle 1.12513 (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 290 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 278 time to evaluate : 2.363 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: A 260 MET cc_start: 0.5894 (mmp) cc_final: 0.5479 (mmt) REVERT: B 97 ILE cc_start: 0.7941 (mt) cc_final: 0.7624 (mt) REVERT: B 270 ASP cc_start: 0.6727 (t0) cc_final: 0.5979 (m-30) REVERT: B 290 PHE cc_start: 0.5882 (t80) cc_final: 0.5675 (t80) REVERT: C 55 SER cc_start: 0.8700 (p) cc_final: 0.8470 (t) REVERT: C 71 LYS cc_start: 0.6071 (tptt) cc_final: 0.5782 (tptt) REVERT: C 75 ASN cc_start: 0.6516 (m-40) cc_final: 0.6170 (m-40) REVERT: C 91 THR cc_start: 0.7815 (m) cc_final: 0.7181 (p) REVERT: C 270 ASP cc_start: 0.6615 (t0) cc_final: 0.6123 (m-30) outliers start: 12 outliers final: 9 residues processed: 284 average time/residue: 0.5664 time to fit residues: 243.5243 Evaluate side-chains 269 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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: 2.9990 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.266437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.214558 restraints weight = 50756.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.223541 restraints weight = 23382.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.228973 restraints weight = 14904.805| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 14880 Z= 0.264 Angle : 1.110 21.607 20172 Z= 0.671 Chirality : 0.046 0.227 2313 Planarity : 0.005 0.048 2568 Dihedral : 5.150 25.782 1971 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.20 % Allowed : 7.22 % Favored : 91.58 % 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: -0.75 (0.20), residues: 1791 helix: -0.84 (0.17), residues: 804 sheet: 0.37 (0.50), residues: 129 loop : -0.09 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 373 HIS 0.010 0.002 HIS A 128 PHE 0.038 0.003 PHE B 352 TYR 0.019 0.002 TYR B 500 ARG 0.004 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 666) hydrogen bonds : angle 5.66063 ( 1845) SS BOND : bond 0.00610 ( 3) SS BOND : angle 1.22542 ( 6) covalent geometry : bond 0.00595 (14877) covalent geometry : angle 1.11043 (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 284 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 2.220 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 91 THR cc_start: 0.7784 (m) cc_final: 0.7206 (p) REVERT: A 176 ASN cc_start: 0.6540 (m-40) cc_final: 0.6287 (m110) REVERT: A 260 MET cc_start: 0.6293 (mmp) cc_final: 0.5514 (mmt) REVERT: B 91 THR cc_start: 0.7936 (m) cc_final: 0.7270 (p) REVERT: B 97 ILE cc_start: 0.8058 (mt) cc_final: 0.7856 (mt) REVERT: B 176 ASN cc_start: 0.6367 (m-40) cc_final: 0.6081 (m110) REVERT: B 270 ASP cc_start: 0.6525 (t0) cc_final: 0.5891 (m-30) REVERT: B 290 PHE cc_start: 0.5773 (t80) cc_final: 0.5556 (t80) REVERT: C 260 MET cc_start: 0.6338 (mmp) cc_final: 0.5906 (mmt) outliers start: 20 outliers final: 16 residues processed: 275 average time/residue: 0.6867 time to fit residues: 288.6073 Evaluate side-chains 272 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 256 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 137 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS B 315 ASN C 66 GLN C 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.260356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.207887 restraints weight = 50932.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.216584 restraints weight = 23811.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.222164 restraints weight = 15322.796| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 14880 Z= 0.344 Angle : 1.167 21.708 20172 Z= 0.701 Chirality : 0.049 0.188 2313 Planarity : 0.006 0.055 2568 Dihedral : 5.558 26.743 1971 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.93 % Allowed : 9.39 % Favored : 88.69 % 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: -1.61 (0.20), residues: 1791 helix: -1.37 (0.16), residues: 828 sheet: 0.09 (0.50), residues: 129 loop : -0.76 (0.23), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 373 HIS 0.015 0.003 HIS C 128 PHE 0.050 0.004 PHE C 352 TYR 0.025 0.003 TYR C 147 ARG 0.005 0.001 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 666) hydrogen bonds : angle 6.05168 ( 1845) SS BOND : bond 0.00994 ( 3) SS BOND : angle 1.51136 ( 6) covalent geometry : bond 0.00782 (14877) covalent geometry : angle 1.16690 (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 292 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 2.280 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: A 66 GLN cc_start: 0.7642 (mp10) cc_final: 0.7373 (mp10) REVERT: A 168 ASN cc_start: 0.5171 (m-40) cc_final: 0.3729 (p0) REVERT: A 176 ASN cc_start: 0.6337 (m-40) cc_final: 0.6102 (m110) REVERT: A 260 MET cc_start: 0.6263 (mmp) cc_final: 0.5625 (mmt) REVERT: A 294 MET cc_start: 0.4522 (mmm) cc_final: 0.4296 (mmm) REVERT: A 374 ASP cc_start: 0.8493 (m-30) cc_final: 0.7816 (m-30) REVERT: B 176 ASN cc_start: 0.6588 (m-40) cc_final: 0.6123 (m110) REVERT: B 270 ASP cc_start: 0.5924 (t0) cc_final: 0.5461 (m-30) REVERT: B 296 TYR cc_start: 0.6943 (m-80) cc_final: 0.6243 (m-80) REVERT: B 374 ASP cc_start: 0.8138 (m-30) cc_final: 0.7911 (m-30) REVERT: C 168 ASN cc_start: 0.4585 (m-40) cc_final: 0.3393 (p0) REVERT: C 260 MET cc_start: 0.6399 (mmp) cc_final: 0.5814 (mmt) REVERT: C 374 ASP cc_start: 0.8343 (m-30) cc_final: 0.7537 (m-30) outliers start: 32 outliers final: 27 residues processed: 276 average time/residue: 0.6176 time to fit residues: 261.9398 Evaluate side-chains 271 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 392 ILE 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 561 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 512 TYR Chi-restraints excluded: chain C residue 561 VAL 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: 0.5980 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.266609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.216625 restraints weight = 50164.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.225541 restraints weight = 22854.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.231263 restraints weight = 14437.288| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14880 Z= 0.159 Angle : 1.067 21.899 20172 Z= 0.645 Chirality : 0.045 0.164 2313 Planarity : 0.005 0.049 2568 Dihedral : 5.140 32.440 1971 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.44 % Allowed : 10.47 % Favored : 88.09 % 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: -0.95 (0.20), residues: 1791 helix: -0.81 (0.18), residues: 798 sheet: 0.19 (0.51), residues: 123 loop : -0.41 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 373 HIS 0.005 0.001 HIS C 319 PHE 0.028 0.002 PHE A 352 TYR 0.022 0.002 TYR B 500 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 666) hydrogen bonds : angle 5.39292 ( 1845) SS BOND : bond 0.00576 ( 3) SS BOND : angle 1.37629 ( 6) covalent geometry : bond 0.00362 (14877) covalent geometry : angle 1.06703 (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 295 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 2.229 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: A 260 MET cc_start: 0.6365 (mmp) cc_final: 0.5676 (mmt) REVERT: A 374 ASP cc_start: 0.8079 (m-30) cc_final: 0.7548 (m-30) REVERT: B 168 ASN cc_start: 0.5022 (m-40) cc_final: 0.3932 (p0) REVERT: B 176 ASN cc_start: 0.6512 (m-40) cc_final: 0.6245 (m110) REVERT: B 270 ASP cc_start: 0.6136 (t0) cc_final: 0.5536 (m-30) REVERT: B 347 LYS cc_start: 0.6959 (mttp) cc_final: 0.6608 (ttpt) REVERT: B 374 ASP cc_start: 0.8029 (m-30) cc_final: 0.7811 (m-30) REVERT: C 168 ASN cc_start: 0.4837 (m-40) cc_final: 0.3583 (p0) REVERT: C 260 MET cc_start: 0.6268 (mmp) cc_final: 0.5712 (mmt) outliers start: 24 outliers final: 20 residues processed: 286 average time/residue: 0.5492 time to fit residues: 239.7164 Evaluate side-chains 279 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 469 LEU 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 176 ASN 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 512 TYR Chi-restraints excluded: chain C residue 561 VAL 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: 0.0050 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.5534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.268205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.218024 restraints weight = 50102.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.226666 restraints weight = 23953.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.232068 restraints weight = 15544.287| |-----------------------------------------------------------------------------| r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.5290 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= 0.150 Angle : 1.067 22.086 20172 Z= 0.645 Chirality : 0.045 0.164 2313 Planarity : 0.004 0.050 2568 Dihedral : 4.982 39.530 1971 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.32 % Allowed : 11.43 % Favored : 87.24 % 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: -0.73 (0.21), residues: 1791 helix: -0.58 (0.18), residues: 795 sheet: 0.25 (0.51), residues: 123 loop : -0.34 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 373 HIS 0.006 0.001 HIS B 117 PHE 0.023 0.002 PHE C 352 TYR 0.021 0.002 TYR B 500 ARG 0.003 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 666) hydrogen bonds : angle 5.18020 ( 1845) SS BOND : bond 0.00489 ( 3) SS BOND : angle 4.75402 ( 6) covalent geometry : bond 0.00341 (14877) covalent geometry : angle 1.06444 (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 298 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 2.382 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: A 260 MET cc_start: 0.6284 (mmp) cc_final: 0.5468 (mmt) REVERT: A 290 PHE cc_start: 0.5350 (t80) cc_final: 0.5116 (t80) REVERT: B 176 ASN cc_start: 0.6603 (m-40) cc_final: 0.6361 (m110) REVERT: B 270 ASP cc_start: 0.6187 (t0) cc_final: 0.5569 (m-30) REVERT: B 316 ILE cc_start: 0.5527 (tp) cc_final: 0.5249 (tp) REVERT: B 347 LYS cc_start: 0.6923 (mttp) cc_final: 0.6452 (ttpp) REVERT: B 374 ASP cc_start: 0.8076 (m-30) cc_final: 0.7840 (m-30) outliers start: 22 outliers final: 20 residues processed: 288 average time/residue: 0.5774 time to fit residues: 253.4437 Evaluate side-chains 283 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 263 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 469 LEU 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 7 ILE Chi-restraints excluded: chain C residue 176 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 172 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 148 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.267093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.217754 restraints weight = 50278.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.226331 restraints weight = 23943.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.231716 restraints weight = 15487.512| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14880 Z= 0.160 Angle : 1.064 22.138 20172 Z= 0.643 Chirality : 0.045 0.173 2313 Planarity : 0.004 0.051 2568 Dihedral : 4.958 37.957 1971 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.56 % Allowed : 11.43 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.80 (0.20), residues: 1791 helix: -0.53 (0.18), residues: 795 sheet: 0.33 (0.52), residues: 123 loop : -0.52 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 373 HIS 0.005 0.001 HIS B 117 PHE 0.025 0.002 PHE C 352 TYR 0.028 0.002 TYR C 381 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 666) hydrogen bonds : angle 5.16829 ( 1845) SS BOND : bond 0.00680 ( 3) SS BOND : angle 1.77493 ( 6) covalent geometry : bond 0.00366 (14877) covalent geometry : angle 1.06364 (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 292 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 2.119 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: 0.6301 (mmp) cc_final: 0.5482 (mmt) REVERT: B 176 ASN cc_start: 0.6652 (m-40) cc_final: 0.6378 (m110) REVERT: B 270 ASP cc_start: 0.6115 (t0) cc_final: 0.5558 (m-30) REVERT: B 316 ILE cc_start: 0.5527 (tp) cc_final: 0.5247 (tp) REVERT: B 347 LYS cc_start: 0.6892 (mttp) cc_final: 0.6641 (ttpt) REVERT: B 374 ASP cc_start: 0.8183 (m-30) cc_final: 0.7945 (m-30) REVERT: B 424 ILE cc_start: 0.7931 (mt) cc_final: 0.7660 (mt) REVERT: C 31 CYS cc_start: 0.1265 (OUTLIER) cc_final: 0.1028 (m) REVERT: C 260 MET cc_start: 0.6276 (mmp) cc_final: 0.5752 (mmt) outliers start: 26 outliers final: 22 residues processed: 280 average time/residue: 0.5601 time to fit residues: 237.2774 Evaluate side-chains 283 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 469 LEU 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 31 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 128 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.272059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.218793 restraints weight = 51557.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.228336 restraints weight = 24006.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.234345 restraints weight = 15426.907| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14880 Z= 0.191 Angle : 1.076 22.039 20172 Z= 0.650 Chirality : 0.045 0.176 2313 Planarity : 0.005 0.052 2568 Dihedral : 5.009 36.013 1971 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.50 % Allowed : 11.97 % Favored : 86.52 % 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: -0.93 (0.20), residues: 1791 helix: -0.63 (0.18), residues: 795 sheet: 0.33 (0.52), residues: 123 loop : -0.61 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 373 HIS 0.006 0.001 HIS A 117 PHE 0.044 0.002 PHE A 290 TYR 0.025 0.002 TYR C 381 ARG 0.004 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 666) hydrogen bonds : angle 5.29819 ( 1845) SS BOND : bond 0.00673 ( 3) SS BOND : angle 2.28134 ( 6) covalent geometry : bond 0.00438 (14877) covalent geometry : angle 1.07588 (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 282 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.6295 (mmp) cc_final: 0.5452 (mmt) REVERT: A 424 ILE cc_start: 0.8003 (mt) cc_final: 0.7376 (mm) REVERT: B 176 ASN cc_start: 0.6466 (m-40) cc_final: 0.6184 (m110) REVERT: B 270 ASP cc_start: 0.6092 (t0) cc_final: 0.5631 (m-30) REVERT: B 296 TYR cc_start: 0.6858 (m-80) cc_final: 0.6318 (m-80) REVERT: C 31 CYS cc_start: 0.2224 (OUTLIER) cc_final: 0.1088 (m) REVERT: C 260 MET cc_start: 0.6227 (mmp) cc_final: 0.5711 (mmt) outliers start: 25 outliers final: 24 residues processed: 273 average time/residue: 0.5530 time to fit residues: 230.5835 Evaluate side-chains 279 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 465 MET 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 7 ILE Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 176 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.279801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.229366 restraints weight = 50983.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.239191 restraints weight = 23015.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.245280 restraints weight = 14485.933| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14880 Z= 0.124 Angle : 1.049 22.302 20172 Z= 0.635 Chirality : 0.044 0.172 2313 Planarity : 0.004 0.052 2568 Dihedral : 4.781 34.798 1971 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.38 % Allowed : 12.03 % Favored : 86.58 % 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: -0.53 (0.21), residues: 1791 helix: -0.34 (0.19), residues: 774 sheet: 0.44 (0.52), residues: 123 loop : -0.33 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 373 HIS 0.004 0.001 HIS B 117 PHE 0.037 0.002 PHE A 290 TYR 0.024 0.001 TYR C 381 ARG 0.003 0.000 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 666) hydrogen bonds : angle 4.99169 ( 1845) SS BOND : bond 0.00459 ( 3) SS BOND : angle 1.40408 ( 6) covalent geometry : bond 0.00283 (14877) covalent geometry : angle 1.04919 (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 285 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 2.193 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: A 260 MET cc_start: 0.6275 (mmp) cc_final: 0.5438 (mmt) REVERT: A 347 LYS cc_start: 0.7065 (ttmt) cc_final: 0.6776 (tttt) REVERT: A 389 MET cc_start: 0.7698 (tpp) cc_final: 0.7183 (tpt) REVERT: B 176 ASN cc_start: 0.6797 (m-40) cc_final: 0.6561 (m110) REVERT: B 270 ASP cc_start: 0.6088 (t0) cc_final: 0.5640 (m-30) REVERT: B 424 ILE cc_start: 0.7861 (mt) cc_final: 0.7594 (mt) REVERT: B 452 MET cc_start: 0.4288 (ttt) cc_final: 0.3892 (ttm) REVERT: B 541 MET cc_start: 0.0549 (ttp) cc_final: 0.0053 (ttp) REVERT: C 31 CYS cc_start: 0.1302 (OUTLIER) cc_final: 0.0516 (m) REVERT: C 260 MET cc_start: 0.6226 (mmp) cc_final: 0.5557 (mmt) outliers start: 23 outliers final: 22 residues processed: 277 average time/residue: 0.5559 time to fit residues: 234.4762 Evaluate side-chains 277 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ARG Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 46 HIS Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 66 GLN A 212 GLN B 39 GLN C 212 GLN C 586 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.268185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.215303 restraints weight = 51283.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.224660 restraints weight = 23942.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.230411 restraints weight = 15343.653| |-----------------------------------------------------------------------------| r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14880 Z= 0.230 Angle : 1.090 22.031 20172 Z= 0.658 Chirality : 0.046 0.175 2313 Planarity : 0.005 0.052 2568 Dihedral : 5.026 34.262 1971 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.38 % Allowed : 12.15 % Favored : 86.46 % 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: -0.96 (0.21), residues: 1791 helix: -0.60 (0.18), residues: 789 sheet: 0.32 (0.51), residues: 123 loop : -0.69 (0.23), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 373 HIS 0.008 0.001 HIS A 117 PHE 0.039 0.003 PHE A 290 TYR 0.021 0.002 TYR B 500 ARG 0.004 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 666) hydrogen bonds : angle 5.39310 ( 1845) SS BOND : bond 0.00646 ( 3) SS BOND : angle 1.85503 ( 6) covalent geometry : bond 0.00526 (14877) covalent geometry : angle 1.08984 (20166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10138.46 seconds wall clock time: 178 minutes 54.32 seconds (10734.32 seconds total)