Starting phenix.real_space_refine on Mon May 12 15:34:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.map" model { file = "/net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yyl_39675/05_2025/8yyl_39675.cif" } resolution = 4.01 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5710 2.51 5 N 1542 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8981 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4517 Classifications: {'peptide': 559} Link IDs: {'PTRANS': 26, 'TRANS': 532} Chain breaks: 10 Chain: "B" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4101 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 6 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 363 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain breaks: 1 Time building chain proxies: 5.62, per 1000 atoms: 0.63 Number of scatterers: 8981 At special positions: 0 Unit cell: (85.8, 139.92, 166.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1668 8.00 N 1542 7.00 C 5710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.04 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 215 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 252 " distance=2.03 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS A 268 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 887 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 41 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 22 sheets defined 15.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.766A pdb=" N HIS A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.569A pdb=" N CYS A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.612A pdb=" N GLU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'B' and resid 342 through 345 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.824A pdb=" N GLU B 356 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 386 removed outlier: 4.447A pdb=" N GLU B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 474 removed outlier: 3.765A pdb=" N ILE B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.586A pdb=" N GLN B 573 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 718 through 741 Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.206A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.591A pdb=" N LEU C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.018A pdb=" N GLU A 33 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE A 56 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS A 35 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.871A pdb=" N MET A 38 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU A 63 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE A 40 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET A 65 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 61 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU A 90 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 63 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A 92 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 92 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU A 120 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU A 147 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 122 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AA7, first strand: chain 'A' and resid 319 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.666A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 338 through 348 removed outlier: 10.666A pdb=" N VAL A 362 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N LEU A 342 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASN A 364 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLY A 344 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N LYS A 396 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 367 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ARG A 398 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE A 369 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 395 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N LEU A 430 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 397 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N HIS A 456 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 429 " --> pdb=" O HIS A 456 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 500 Processing sheet with id=AB2, first strand: chain 'A' and resid 502 through 507 removed outlier: 6.697A pdb=" N ARG A 515 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 505 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 513 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 557 through 561 Processing sheet with id=AB4, first strand: chain 'B' and resid 338 through 340 removed outlier: 6.548A pdb=" N CYS B 339 " --> pdb=" O ASN B 364 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 391 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.578A pdb=" N ARG B 398 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B 395 " --> pdb=" O TYR B 428 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU B 430 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 397 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N HIS B 456 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 429 " --> pdb=" O HIS B 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 499 through 500 Processing sheet with id=AB7, first strand: chain 'B' and resid 511 through 515 removed outlier: 3.694A pdb=" N ILE B 512 " --> pdb=" O MET B 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 580 " --> pdb=" O ILE B 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 561 removed outlier: 4.098A pdb=" N GLY B 529 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 626 through 634 removed outlier: 6.741A pdb=" N LYS B 641 " --> pdb=" O PRO B 628 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER B 630 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 639 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 632 " --> pdb=" O GLN B 637 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLN B 637 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 786 through 790 removed outlier: 4.271A pdb=" N GLN B 815 " --> pdb=" O ARG B 821 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 821 " --> pdb=" O GLN B 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 786 through 790 Processing sheet with id=AC3, first strand: chain 'B' and resid 846 through 849 Processing sheet with id=AC4, first strand: chain 'B' and resid 883 through 889 removed outlier: 3.543A pdb=" N LEU B 871 " --> pdb=" O THR B 916 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 606 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: 2.93 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2899 1.34 - 1.46: 2171 1.46 - 1.59: 4040 1.59 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 9185 Sorted by residual: bond pdb=" N GLY B 365 " pdb=" CA GLY B 365 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.77e+00 bond pdb=" CG1 ILE C 32 " pdb=" CD1 ILE C 32 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" C GLY B 365 " pdb=" O GLY B 365 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.35e-02 5.49e+03 2.68e+00 bond pdb=" C ALA B 537 " pdb=" O ALA B 537 " ideal model delta sigma weight residual 1.244 1.230 0.014 1.00e-02 1.00e+04 1.96e+00 bond pdb=" CA GLY B 365 " pdb=" C GLY B 365 " ideal model delta sigma weight residual 1.514 1.534 -0.019 1.41e-02 5.03e+03 1.91e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12101 1.85 - 3.71: 268 3.71 - 5.56: 38 5.56 - 7.42: 11 7.42 - 9.27: 5 Bond angle restraints: 12423 Sorted by residual: angle pdb=" N THR A 68 " pdb=" CA THR A 68 " pdb=" C THR A 68 " ideal model delta sigma weight residual 110.50 117.25 -6.75 1.41e+00 5.03e-01 2.29e+01 angle pdb=" N ASN B 376 " pdb=" CA ASN B 376 " pdb=" C ASN B 376 " ideal model delta sigma weight residual 110.91 106.38 4.53 1.17e+00 7.31e-01 1.50e+01 angle pdb=" C ASP B 647 " pdb=" N PRO B 648 " pdb=" CA PRO B 648 " ideal model delta sigma weight residual 119.56 115.69 3.87 1.01e+00 9.80e-01 1.47e+01 angle pdb=" CA MET A 321 " pdb=" CB MET A 321 " pdb=" CG MET A 321 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.62e+00 angle pdb=" N GLY B 365 " pdb=" CA GLY B 365 " pdb=" C GLY B 365 " ideal model delta sigma weight residual 113.18 106.55 6.63 2.37e+00 1.78e-01 7.82e+00 ... (remaining 12418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4847 17.90 - 35.81: 529 35.81 - 53.71: 123 53.71 - 71.61: 24 71.61 - 89.51: 9 Dihedral angle restraints: 5532 sinusoidal: 2306 harmonic: 3226 Sorted by residual: dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 53 " pdb=" CB CYS A 53 " ideal model delta sinusoidal sigma weight residual 93.00 45.30 47.70 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 215 " pdb=" CB CYS A 215 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 50 " pdb=" CB CYS C 50 " ideal model delta sinusoidal sigma weight residual -86.00 -127.50 41.50 1 1.00e+01 1.00e-02 2.41e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 893 0.037 - 0.074: 298 0.074 - 0.111: 122 0.111 - 0.149: 30 0.149 - 0.186: 7 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE B 415 " pdb=" CA ILE B 415 " pdb=" CG1 ILE B 415 " pdb=" CG2 ILE B 415 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CB ILE B 369 " pdb=" CA ILE B 369 " pdb=" CG1 ILE B 369 " pdb=" CG2 ILE B 369 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB ILE B 512 " pdb=" CA ILE B 512 " pdb=" CG1 ILE B 512 " pdb=" CG2 ILE B 512 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1347 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 517 " -0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO A 518 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 521 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 522 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 258 " 0.013 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE A 258 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 258 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 258 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 258 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 258 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 258 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 530 2.73 - 3.27: 8896 3.27 - 3.81: 14968 3.81 - 4.36: 18130 4.36 - 4.90: 29967 Nonbonded interactions: 72491 Sorted by model distance: nonbonded pdb=" NZ LYS A 294 " pdb=" OD1 ASN A 295 " model vdw 2.185 3.120 nonbonded pdb=" O LYS B 584 " pdb=" OG1 THR B 587 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP A 440 " pdb=" OG SER A 442 " model vdw 2.221 3.040 nonbonded pdb=" N GLU B 465 " pdb=" OE1 GLU B 465 " model vdw 2.222 3.120 nonbonded pdb=" OG SER A 244 " pdb=" O LYS A 251 " model vdw 2.234 3.040 ... (remaining 72486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.300 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 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 : 0.004 0.066 9206 Z= 0.171 Angle : 0.701 9.272 12465 Z= 0.383 Chirality : 0.046 0.186 1350 Planarity : 0.005 0.093 1591 Dihedral : 15.498 89.513 3385 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.10 % Allowed : 18.96 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.25), residues: 1071 helix: -0.36 (0.44), residues: 134 sheet: 0.12 (0.33), residues: 263 loop : -0.67 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 441 HIS 0.018 0.002 HIS C 5 PHE 0.054 0.002 PHE A 258 TYR 0.028 0.002 TYR A 118 ARG 0.007 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.19349 ( 219) hydrogen bonds : angle 8.25458 ( 606) SS BOND : bond 0.00426 ( 21) SS BOND : angle 1.03393 ( 42) covalent geometry : bond 0.00351 ( 9185) covalent geometry : angle 0.69970 (12423) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.024 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: A 204 GLN cc_start: 0.8433 (tp-100) cc_final: 0.8216 (tp40) REVERT: A 580 MET cc_start: 0.5289 (pmm) cc_final: 0.5062 (pmm) REVERT: B 616 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7090 (mm-40) REVERT: B 839 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5475 (m-30) REVERT: B 891 LYS cc_start: 0.5688 (mmpt) cc_final: 0.5412 (mmpt) outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.2605 time to fit residues: 34.5910 Evaluate side-chains 63 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS A 375 ASN B 467 HIS B 492 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 662 GLN B 738 ASN B 802 HIS ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.104830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.076510 restraints weight = 47990.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.076037 restraints weight = 38713.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075568 restraints weight = 30650.462| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9206 Z= 0.201 Angle : 0.639 9.628 12465 Z= 0.332 Chirality : 0.046 0.167 1350 Planarity : 0.005 0.076 1591 Dihedral : 4.748 21.879 1205 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.26), residues: 1071 helix: -0.13 (0.45), residues: 139 sheet: 0.38 (0.32), residues: 271 loop : -0.60 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 441 HIS 0.008 0.001 HIS A 274 PHE 0.022 0.002 PHE A 258 TYR 0.018 0.002 TYR A 118 ARG 0.010 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 219) hydrogen bonds : angle 6.23780 ( 606) SS BOND : bond 0.00729 ( 21) SS BOND : angle 1.34875 ( 42) covalent geometry : bond 0.00437 ( 9185) covalent geometry : angle 0.63566 (12423) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.951 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 outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2603 time to fit residues: 28.3183 Evaluate side-chains 53 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 104 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 291 HIS A 307 HIS B 575 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.102603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.077097 restraints weight = 51253.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.077071 restraints weight = 42351.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.077060 restraints weight = 31221.798| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9206 Z= 0.229 Angle : 0.637 10.253 12465 Z= 0.332 Chirality : 0.045 0.179 1350 Planarity : 0.005 0.101 1591 Dihedral : 4.989 28.908 1205 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.25), residues: 1071 helix: -0.05 (0.46), residues: 134 sheet: 0.08 (0.32), residues: 258 loop : -0.74 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 924 HIS 0.005 0.001 HIS B 467 PHE 0.018 0.002 PHE A 258 TYR 0.016 0.002 TYR A 118 ARG 0.016 0.001 ARG B 914 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 219) hydrogen bonds : angle 6.26371 ( 606) SS BOND : bond 0.00477 ( 21) SS BOND : angle 1.22322 ( 42) covalent geometry : bond 0.00507 ( 9185) covalent geometry : angle 0.63419 (12423) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.944 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: B 455 PHE cc_start: 0.9053 (m-80) cc_final: 0.8826 (m-80) REVERT: B 810 LEU cc_start: 0.8904 (tp) cc_final: 0.8444 (pp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2478 time to fit residues: 23.4477 Evaluate side-chains 49 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 66 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.104039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078806 restraints weight = 50469.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078549 restraints weight = 42353.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079320 restraints weight = 29868.693| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9206 Z= 0.119 Angle : 0.550 10.148 12465 Z= 0.285 Chirality : 0.044 0.147 1350 Planarity : 0.004 0.067 1591 Dihedral : 4.690 25.183 1205 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1071 helix: 0.13 (0.47), residues: 136 sheet: 0.20 (0.32), residues: 250 loop : -0.66 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 441 HIS 0.007 0.001 HIS A 291 PHE 0.013 0.001 PHE A 258 TYR 0.022 0.001 TYR A 457 ARG 0.008 0.001 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 219) hydrogen bonds : angle 5.93461 ( 606) SS BOND : bond 0.00324 ( 21) SS BOND : angle 1.07078 ( 42) covalent geometry : bond 0.00269 ( 9185) covalent geometry : angle 0.54723 (12423) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.104 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: A 137 MET cc_start: 0.8638 (mmt) cc_final: 0.8171 (tpp) REVERT: A 531 MET cc_start: 0.7800 (mpp) cc_final: 0.7590 (mpp) REVERT: A 533 PHE cc_start: 0.9042 (m-80) cc_final: 0.8831 (m-80) REVERT: B 810 LEU cc_start: 0.8828 (tp) cc_final: 0.8381 (pp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2393 time to fit residues: 22.6073 Evaluate side-chains 55 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.0270 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 overall best weight: 0.8878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN A 575 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.103319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.077831 restraints weight = 49552.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.077508 restraints weight = 39980.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.076929 restraints weight = 30513.017| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9206 Z= 0.125 Angle : 0.544 9.692 12465 Z= 0.281 Chirality : 0.044 0.204 1350 Planarity : 0.003 0.051 1591 Dihedral : 4.542 24.468 1205 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.25), residues: 1071 helix: 0.12 (0.46), residues: 137 sheet: 0.09 (0.33), residues: 244 loop : -0.64 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 441 HIS 0.005 0.001 HIS A 291 PHE 0.011 0.001 PHE A 258 TYR 0.013 0.001 TYR A 118 ARG 0.008 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 219) hydrogen bonds : angle 5.64596 ( 606) SS BOND : bond 0.00363 ( 21) SS BOND : angle 0.99461 ( 42) covalent geometry : bond 0.00283 ( 9185) covalent geometry : angle 0.54198 (12423) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.056 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: A 137 MET cc_start: 0.8682 (mmt) cc_final: 0.8214 (tpp) REVERT: B 810 LEU cc_start: 0.8838 (tp) cc_final: 0.8405 (pp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2333 time to fit residues: 21.8092 Evaluate side-chains 51 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 85 optimal weight: 0.0870 chunk 69 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 49 optimal weight: 8.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.104591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080575 restraints weight = 51176.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.080936 restraints weight = 41828.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081063 restraints weight = 28504.703| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9206 Z= 0.091 Angle : 0.520 9.540 12465 Z= 0.265 Chirality : 0.044 0.201 1350 Planarity : 0.003 0.048 1591 Dihedral : 4.354 23.848 1205 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.25), residues: 1071 helix: 0.00 (0.46), residues: 141 sheet: 0.20 (0.34), residues: 233 loop : -0.65 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 441 HIS 0.004 0.001 HIS B 737 PHE 0.013 0.001 PHE B 455 TYR 0.026 0.001 TYR A 457 ARG 0.005 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 219) hydrogen bonds : angle 5.42174 ( 606) SS BOND : bond 0.00232 ( 21) SS BOND : angle 0.84430 ( 42) covalent geometry : bond 0.00201 ( 9185) covalent geometry : angle 0.51831 (12423) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.053 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: A 137 MET cc_start: 0.8592 (mmt) cc_final: 0.8107 (tpp) REVERT: A 531 MET cc_start: 0.7825 (mpp) cc_final: 0.7583 (mpp) REVERT: A 533 PHE cc_start: 0.9134 (m-80) cc_final: 0.8884 (m-80) REVERT: B 810 LEU cc_start: 0.8767 (tp) cc_final: 0.8354 (pp) REVERT: B 893 PHE cc_start: 0.7771 (t80) cc_final: 0.7438 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2160 time to fit residues: 22.2031 Evaluate side-chains 54 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 52 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.104178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079462 restraints weight = 51331.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.080354 restraints weight = 39402.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080050 restraints weight = 28186.000| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9206 Z= 0.098 Angle : 0.505 8.880 12465 Z= 0.260 Chirality : 0.044 0.165 1350 Planarity : 0.003 0.041 1591 Dihedral : 4.253 24.361 1205 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.10 % Allowed : 0.90 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.25), residues: 1071 helix: -0.05 (0.45), residues: 144 sheet: 0.40 (0.34), residues: 216 loop : -0.66 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 441 HIS 0.005 0.001 HIS B 737 PHE 0.008 0.001 PHE A 258 TYR 0.020 0.001 TYR A 457 ARG 0.008 0.000 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 219) hydrogen bonds : angle 5.30677 ( 606) SS BOND : bond 0.00241 ( 21) SS BOND : angle 0.92523 ( 42) covalent geometry : bond 0.00222 ( 9185) covalent geometry : angle 0.50347 (12423) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.026 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: A 137 MET cc_start: 0.8620 (mmt) cc_final: 0.8147 (tpp) REVERT: A 533 PHE cc_start: 0.9123 (m-80) cc_final: 0.8845 (m-80) REVERT: B 810 LEU cc_start: 0.8857 (tp) cc_final: 0.8440 (pp) REVERT: B 893 PHE cc_start: 0.7807 (t80) cc_final: 0.7509 (t80) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.2464 time to fit residues: 24.6674 Evaluate side-chains 53 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 0.0670 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 overall best weight: 1.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 458 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.101761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.076544 restraints weight = 50009.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.075590 restraints weight = 36020.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.075820 restraints weight = 32385.112| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9206 Z= 0.162 Angle : 0.575 8.716 12465 Z= 0.294 Chirality : 0.045 0.305 1350 Planarity : 0.004 0.058 1591 Dihedral : 4.529 24.709 1205 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.25), residues: 1071 helix: 0.19 (0.46), residues: 138 sheet: 0.02 (0.34), residues: 235 loop : -0.67 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 441 HIS 0.005 0.001 HIS B 467 PHE 0.020 0.001 PHE A 455 TYR 0.012 0.001 TYR A 428 ARG 0.010 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 219) hydrogen bonds : angle 5.43937 ( 606) SS BOND : bond 0.00360 ( 21) SS BOND : angle 1.04417 ( 42) covalent geometry : bond 0.00366 ( 9185) covalent geometry : angle 0.57303 (12423) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.934 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: A 137 MET cc_start: 0.8711 (mmt) cc_final: 0.8225 (tpp) REVERT: A 533 PHE cc_start: 0.9150 (m-80) cc_final: 0.8824 (m-80) REVERT: B 810 LEU cc_start: 0.8918 (tp) cc_final: 0.8406 (pp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.2331 time to fit residues: 22.6917 Evaluate side-chains 53 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 0.0060 chunk 101 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.103191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.079218 restraints weight = 51441.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.078241 restraints weight = 37405.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.078340 restraints weight = 35044.817| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9206 Z= 0.105 Angle : 0.523 9.064 12465 Z= 0.268 Chirality : 0.044 0.311 1350 Planarity : 0.003 0.056 1591 Dihedral : 4.378 21.838 1205 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.10 % Allowed : 0.50 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.25), residues: 1071 helix: 0.23 (0.46), residues: 143 sheet: 0.06 (0.34), residues: 230 loop : -0.66 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.010 0.001 PHE A 455 TYR 0.011 0.001 TYR A 534 ARG 0.008 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.02704 ( 219) hydrogen bonds : angle 5.30092 ( 606) SS BOND : bond 0.00271 ( 21) SS BOND : angle 0.87129 ( 42) covalent geometry : bond 0.00238 ( 9185) covalent geometry : angle 0.52156 (12423) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.962 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: A 137 MET cc_start: 0.8653 (mmt) cc_final: 0.8167 (tpp) REVERT: A 431 ASP cc_start: 0.8479 (t0) cc_final: 0.8090 (t0) REVERT: A 533 PHE cc_start: 0.9168 (m-80) cc_final: 0.8782 (m-80) REVERT: B 810 LEU cc_start: 0.8907 (tp) cc_final: 0.8442 (pp) REVERT: B 869 ILE cc_start: 0.7838 (mm) cc_final: 0.7577 (tp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2221 time to fit residues: 22.0838 Evaluate side-chains 52 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 588 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.100624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075037 restraints weight = 50932.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.074215 restraints weight = 37676.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.074103 restraints weight = 34793.188| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9206 Z= 0.180 Angle : 0.603 9.231 12465 Z= 0.309 Chirality : 0.045 0.279 1350 Planarity : 0.004 0.060 1591 Dihedral : 4.711 21.464 1205 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.25), residues: 1071 helix: 0.43 (0.46), residues: 139 sheet: -0.11 (0.33), residues: 242 loop : -0.68 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 441 HIS 0.005 0.001 HIS B 467 PHE 0.020 0.002 PHE A 455 TYR 0.015 0.001 TYR A 534 ARG 0.006 0.001 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 219) hydrogen bonds : angle 5.54231 ( 606) SS BOND : bond 0.00390 ( 21) SS BOND : angle 1.08608 ( 42) covalent geometry : bond 0.00404 ( 9185) covalent geometry : angle 0.60051 (12423) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8645 (mmt) cc_final: 0.8189 (tpp) REVERT: A 431 ASP cc_start: 0.8473 (t0) cc_final: 0.8105 (t0) REVERT: A 533 PHE cc_start: 0.9175 (m-80) cc_final: 0.8842 (m-80) REVERT: B 526 ASP cc_start: 0.9417 (m-30) cc_final: 0.9206 (m-30) REVERT: B 810 LEU cc_start: 0.9005 (tp) cc_final: 0.8405 (pp) REVERT: B 869 ILE cc_start: 0.7863 (mm) cc_final: 0.7639 (tp) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2294 time to fit residues: 22.6881 Evaluate side-chains 51 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.101898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077321 restraints weight = 51308.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076062 restraints weight = 37708.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.076270 restraints weight = 34117.968| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9206 Z= 0.106 Angle : 0.533 9.053 12465 Z= 0.272 Chirality : 0.044 0.290 1350 Planarity : 0.003 0.056 1591 Dihedral : 4.459 19.191 1205 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.10 % Allowed : 0.20 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.25), residues: 1071 helix: 0.46 (0.46), residues: 139 sheet: -0.09 (0.33), residues: 245 loop : -0.65 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 441 HIS 0.004 0.001 HIS A 274 PHE 0.008 0.001 PHE A 258 TYR 0.014 0.001 TYR A 534 ARG 0.007 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 219) hydrogen bonds : angle 5.36811 ( 606) SS BOND : bond 0.00265 ( 21) SS BOND : angle 0.86179 ( 42) covalent geometry : bond 0.00242 ( 9185) covalent geometry : angle 0.53157 (12423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.32 seconds wall clock time: 56 minutes 53.04 seconds (3413.04 seconds total)