Starting phenix.real_space_refine on Thu Mar 13 06:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.map" model { file = "/net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nur_0520/03_2025/6nur_0520.cif" } resolution = 3.1 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= 0.008 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 Zn 2 6.06 5 S 67 5.16 5 C 5506 2.51 5 N 1451 2.21 5 O 1621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6377 Classifications: {'peptide': 793} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 766} Chain breaks: 1 Chain: "B" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 540 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1521 SG CYS A 301 40.080 60.791 35.896 1.00 1.02 S ATOM 1562 SG CYS A 306 40.063 59.481 33.140 1.00 0.00 S ATOM 1594 SG CYS A 310 43.007 59.321 35.327 1.00 0.24 S ATOM 3002 SG CYS A 487 22.083 57.548 45.278 1.00 25.56 S ATOM 4255 SG CYS A 645 20.457 57.697 42.141 1.00 16.61 S ATOM 4261 SG CYS A 646 24.056 59.797 43.075 1.00 22.36 S Time building chain proxies: 6.38, per 1000 atoms: 0.74 Number of scatterers: 8647 At special positions: 0 Unit cell: (88.55, 92, 128.8, 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) Zn 2 29.99 S 67 16.00 O 1621 8.00 N 1451 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 53.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.963A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.752A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.841A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.670A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 517 removed outlier: 4.036A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 5.037A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.406A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.817A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.949A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.775A pdb=" N THR A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'B' and resid 78 through 99 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.766A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'D' and resid 85 through 99 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.625A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY A 203 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.428A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 345 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.827A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.827A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.462A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1182 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: 3.02 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1734 1.32 - 1.45: 2564 1.45 - 1.58: 4414 1.58 - 1.71: 19 1.71 - 1.84: 102 Bond restraints: 8833 Sorted by residual: bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.371 -0.045 1.10e-02 8.26e+03 1.67e+01 bond pdb=" CB ASN A 657 " pdb=" CG ASN A 657 " ideal model delta sigma weight residual 1.516 1.417 0.099 2.50e-02 1.60e+03 1.58e+01 bond pdb=" CA PRO A 322 " pdb=" C PRO A 322 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.52e+01 bond pdb=" CB HIS C 36 " pdb=" CG HIS C 36 " ideal model delta sigma weight residual 1.497 1.444 0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" NE1 TRP A 290 " pdb=" CE2 TRP A 290 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.39e+01 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 10256 2.08 - 4.16: 1482 4.16 - 6.23: 217 6.23 - 8.31: 39 8.31 - 10.39: 4 Bond angle restraints: 11998 Sorted by residual: angle pdb=" CA PHE A 441 " pdb=" CB PHE A 441 " pdb=" CG PHE A 441 " ideal model delta sigma weight residual 113.80 122.17 -8.37 1.00e+00 1.00e+00 7.00e+01 angle pdb=" C PRO A 322 " pdb=" N PRO A 323 " pdb=" CA PRO A 323 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.01e+00 9.80e-01 6.50e+01 angle pdb=" C ASN A 168 " pdb=" N PRO A 169 " pdb=" CA PRO A 169 " ideal model delta sigma weight residual 119.82 127.15 -7.33 9.80e-01 1.04e+00 5.59e+01 angle pdb=" N ILE A 757 " pdb=" CA ILE A 757 " pdb=" C ILE A 757 " ideal model delta sigma weight residual 108.11 118.50 -10.39 1.40e+00 5.10e-01 5.51e+01 angle pdb=" CA ASP A 846 " pdb=" CB ASP A 846 " pdb=" CG ASP A 846 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.00e+00 1.00e+00 5.31e+01 ... (remaining 11993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 5067 17.30 - 34.60: 150 34.60 - 51.89: 29 51.89 - 69.19: 23 69.19 - 86.49: 5 Dihedral angle restraints: 5274 sinusoidal: 2054 harmonic: 3220 Sorted by residual: dihedral pdb=" C PHE A 441 " pdb=" N PHE A 441 " pdb=" CA PHE A 441 " pdb=" CB PHE A 441 " ideal model delta harmonic sigma weight residual -122.60 -113.94 -8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C PHE D 92 " pdb=" N PHE D 92 " pdb=" CA PHE D 92 " pdb=" CB PHE D 92 " ideal model delta harmonic sigma weight residual -122.60 -131.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 583 " pdb=" CD ARG A 583 " pdb=" NE ARG A 583 " pdb=" CZ ARG A 583 " ideal model delta sinusoidal sigma weight residual 90.00 44.09 45.91 2 1.50e+01 4.44e-03 1.10e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 782 0.070 - 0.140: 405 0.140 - 0.210: 128 0.210 - 0.279: 33 0.279 - 0.349: 8 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CA MET A 242 " pdb=" N MET A 242 " pdb=" C MET A 242 " pdb=" CB MET A 242 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PHE D 92 " pdb=" N PHE D 92 " pdb=" C PHE D 92 " pdb=" CB PHE D 92 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 136 " pdb=" N GLU A 136 " pdb=" C GLU A 136 " pdb=" CB GLU A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1353 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 546 " 0.067 2.00e-02 2.50e+03 3.55e-02 2.52e+01 pdb=" CG TYR A 546 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 546 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 546 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 546 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 546 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 546 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 546 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 515 " -0.057 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR A 515 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 515 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 515 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 515 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 515 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 515 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 515 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 217 " -0.049 2.00e-02 2.50e+03 2.86e-02 1.63e+01 pdb=" CG TYR A 217 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 217 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 217 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 217 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 217 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 217 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 217 " -0.050 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2254 2.80 - 3.32: 8108 3.32 - 3.85: 14981 3.85 - 4.37: 18295 4.37 - 4.90: 29735 Nonbonded interactions: 73373 Sorted by model distance: nonbonded pdb=" O CYS A 645 " pdb="ZN ZN A1002 " model vdw 2.270 2.230 nonbonded pdb=" OD2 ASP C 5 " pdb=" NZ LYS D 97 " model vdw 2.354 3.120 nonbonded pdb=" O ARG A 733 " pdb=" C ASN A 734 " model vdw 2.366 3.270 nonbonded pdb=" OD2 ASP A 258 " pdb=" NZ LYS A 263 " model vdw 2.422 3.120 nonbonded pdb=" N ASP B 112 " pdb=" OD1 ASP B 112 " model vdw 2.424 3.120 ... (remaining 73368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 84 through 191) selection = (chain 'D' and resid 84 through 191) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.760 Find NCS groups from input model: 0.160 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.016 0.111 8833 Z= 1.012 Angle : 1.552 10.388 11998 Z= 1.078 Chirality : 0.092 0.349 1356 Planarity : 0.008 0.038 1537 Dihedral : 10.589 86.487 3192 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.52 % Allowed : 0.73 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.12 (0.23), residues: 1077 helix: -0.42 (0.20), residues: 478 sheet: 0.74 (0.47), residues: 98 loop : 0.33 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.009 TRP A 509 HIS 0.014 0.002 HIS A 613 PHE 0.037 0.006 PHE A 441 TYR 0.067 0.008 TYR A 546 ARG 0.008 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 285 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7938 (m-40) cc_final: 0.7552 (m-40) REVERT: A 183 ARG cc_start: 0.8177 (ptm-80) cc_final: 0.7717 (ttt-90) REVERT: A 583 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8317 (mtt90) REVERT: A 733 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6901 (mmt180) REVERT: A 739 HIS cc_start: 0.8393 (m-70) cc_final: 0.8054 (m90) REVERT: C 25 SER cc_start: 0.7705 (t) cc_final: 0.7490 (p) outliers start: 5 outliers final: 2 residues processed: 290 average time/residue: 0.2683 time to fit residues: 103.8123 Evaluate side-chains 175 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 785 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 705 ASN A 734 ASN A 910 ASN B 104 ASN C 34 GLN C 63 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117885 restraints weight = 10287.828| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.84 r_work: 0.3205 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8833 Z= 0.204 Angle : 0.592 6.706 11998 Z= 0.322 Chirality : 0.044 0.162 1356 Planarity : 0.004 0.042 1537 Dihedral : 5.498 54.950 1196 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.30 % Allowed : 7.96 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.47 (0.25), residues: 1077 helix: 0.56 (0.23), residues: 503 sheet: 0.31 (0.49), residues: 116 loop : 0.23 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 509 HIS 0.006 0.001 HIS A 642 PHE 0.018 0.002 PHE A 652 TYR 0.021 0.002 TYR A 867 ARG 0.005 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 370 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: A 633 MET cc_start: 0.8660 (tmm) cc_final: 0.8407 (ttp) REVERT: A 659 CYS cc_start: 0.8689 (m) cc_final: 0.8360 (m) REVERT: A 743 ASP cc_start: 0.8647 (m-30) cc_final: 0.8447 (m-30) REVERT: A 826 TYR cc_start: 0.8359 (m-80) cc_final: 0.8070 (m-80) REVERT: A 889 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7651 (mtt-85) REVERT: A 915 ARG cc_start: 0.7650 (ptt90) cc_final: 0.7350 (ptt90) REVERT: A 918 GLU cc_start: 0.8613 (tt0) cc_final: 0.8339 (tt0) REVERT: B 158 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: C 59 LEU cc_start: 0.7852 (tp) cc_final: 0.7584 (tt) outliers start: 22 outliers final: 16 residues processed: 203 average time/residue: 0.2465 time to fit residues: 66.9112 Evaluate side-chains 180 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 158 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN D 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.109739 restraints weight = 10541.833| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.81 r_work: 0.3074 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 8833 Z= 0.294 Angle : 0.563 8.232 11998 Z= 0.301 Chirality : 0.044 0.224 1356 Planarity : 0.004 0.060 1537 Dihedral : 5.141 57.529 1191 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.62 % Allowed : 9.11 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.25), residues: 1077 helix: 0.83 (0.23), residues: 505 sheet: 0.32 (0.52), residues: 98 loop : -0.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 509 HIS 0.006 0.001 HIS A 439 PHE 0.017 0.002 PHE D 92 TYR 0.026 0.002 TYR A 867 ARG 0.004 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8867 (mt) REVERT: A 497 ASN cc_start: 0.6893 (t0) cc_final: 0.6073 (p0) REVERT: A 631 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8432 (tmt170) REVERT: A 633 MET cc_start: 0.8790 (tmm) cc_final: 0.8569 (ttp) REVERT: A 681 SER cc_start: 0.8461 (t) cc_final: 0.8107 (p) REVERT: A 743 ASP cc_start: 0.8675 (m-30) cc_final: 0.8356 (m-30) REVERT: A 915 ARG cc_start: 0.7826 (ptt90) cc_final: 0.7235 (ptt90) REVERT: A 918 GLU cc_start: 0.8728 (tt0) cc_final: 0.8484 (tt0) REVERT: B 158 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: D 98 LEU cc_start: 0.8034 (mp) cc_final: 0.7800 (mp) outliers start: 25 outliers final: 20 residues processed: 179 average time/residue: 0.2303 time to fit residues: 55.5892 Evaluate side-chains 178 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 439 HIS A 613 HIS A 791 ASN B 179 ASN C 36 HIS D 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102726 restraints weight = 10552.601| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.74 r_work: 0.2984 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8833 Z= 0.454 Angle : 0.662 11.739 11998 Z= 0.351 Chirality : 0.048 0.200 1356 Planarity : 0.005 0.053 1537 Dihedral : 5.367 58.432 1191 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.46 % Allowed : 7.75 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.08 (0.25), residues: 1077 helix: 0.45 (0.23), residues: 514 sheet: 0.18 (0.50), residues: 95 loop : -0.56 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 509 HIS 0.009 0.002 HIS A 572 PHE 0.020 0.003 PHE A 165 TYR 0.024 0.003 TYR A 867 ARG 0.005 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7157 (t0) cc_final: 0.6434 (p0) REVERT: A 517 ASP cc_start: 0.7974 (m-30) cc_final: 0.7598 (m-30) REVERT: A 588 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8491 (m) REVERT: A 633 MET cc_start: 0.8795 (tmm) cc_final: 0.8504 (ttp) REVERT: A 681 SER cc_start: 0.8935 (t) cc_final: 0.8670 (p) REVERT: A 743 ASP cc_start: 0.8825 (m-30) cc_final: 0.8554 (m-30) REVERT: A 755 MET cc_start: 0.9318 (mtm) cc_final: 0.9105 (mtt) REVERT: A 825 ASP cc_start: 0.7284 (t0) cc_final: 0.7044 (p0) REVERT: A 892 HIS cc_start: 0.7453 (t-90) cc_final: 0.7231 (t-170) REVERT: A 915 ARG cc_start: 0.7859 (ptt90) cc_final: 0.7581 (ptt90) REVERT: A 918 GLU cc_start: 0.8786 (tt0) cc_final: 0.8564 (tt0) REVERT: B 158 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: D 97 LYS cc_start: 0.7193 (tmtt) cc_final: 0.6958 (ttpp) REVERT: D 98 LEU cc_start: 0.7931 (mp) cc_final: 0.7497 (mp) REVERT: D 117 LEU cc_start: 0.6770 (mm) cc_final: 0.6524 (mt) outliers start: 33 outliers final: 28 residues processed: 195 average time/residue: 0.2426 time to fit residues: 62.9188 Evaluate side-chains 183 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain C residue 10 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 360 ASN A 790 ASN D 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106998 restraints weight = 10470.393| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.3043 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8833 Z= 0.180 Angle : 0.505 7.652 11998 Z= 0.269 Chirality : 0.041 0.158 1356 Planarity : 0.004 0.043 1537 Dihedral : 4.976 56.169 1191 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.51 % Allowed : 9.95 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.29 (0.26), residues: 1077 helix: 0.82 (0.24), residues: 513 sheet: -0.15 (0.49), residues: 101 loop : -0.32 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.003 0.001 HIS A 572 PHE 0.016 0.001 PHE A 881 TYR 0.016 0.001 TYR A 867 ARG 0.007 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7164 (t0) cc_final: 0.6413 (p0) REVERT: A 515 TYR cc_start: 0.8950 (m-80) cc_final: 0.8686 (m-80) REVERT: A 588 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 633 MET cc_start: 0.8780 (tmm) cc_final: 0.8473 (ttp) REVERT: A 703 ASN cc_start: 0.8812 (m-40) cc_final: 0.8545 (m110) REVERT: A 743 ASP cc_start: 0.8785 (m-30) cc_final: 0.8450 (m-30) REVERT: A 825 ASP cc_start: 0.7287 (t0) cc_final: 0.7014 (p0) REVERT: B 158 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: C 3 MET cc_start: 0.7656 (mmm) cc_final: 0.7440 (tpp) REVERT: D 97 LYS cc_start: 0.7221 (tmtt) cc_final: 0.6951 (ttpt) REVERT: D 98 LEU cc_start: 0.7802 (mt) cc_final: 0.7558 (mp) REVERT: D 117 LEU cc_start: 0.6692 (mm) cc_final: 0.6471 (mt) outliers start: 24 outliers final: 18 residues processed: 182 average time/residue: 0.2257 time to fit residues: 55.1548 Evaluate side-chains 183 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 158 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 89 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108712 restraints weight = 10284.509| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.76 r_work: 0.3078 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8833 Z= 0.160 Angle : 0.493 8.917 11998 Z= 0.261 Chirality : 0.040 0.153 1356 Planarity : 0.004 0.054 1537 Dihedral : 4.650 56.161 1187 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.51 % Allowed : 10.58 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.46 (0.26), residues: 1077 helix: 0.98 (0.24), residues: 514 sheet: -0.15 (0.45), residues: 119 loop : -0.24 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.013 0.001 HIS A 892 PHE 0.015 0.001 PHE A 881 TYR 0.015 0.001 TYR A 867 ARG 0.013 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7175 (t0) cc_final: 0.6426 (p0) REVERT: A 515 TYR cc_start: 0.8896 (m-80) cc_final: 0.8570 (m-80) REVERT: A 588 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (m) REVERT: A 633 MET cc_start: 0.8806 (tmm) cc_final: 0.8473 (ttp) REVERT: A 703 ASN cc_start: 0.8809 (m-40) cc_final: 0.8527 (m110) REVERT: A 743 ASP cc_start: 0.8726 (m-30) cc_final: 0.8449 (m-30) REVERT: A 825 ASP cc_start: 0.7283 (t0) cc_final: 0.6988 (p0) REVERT: B 158 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: C 3 MET cc_start: 0.7448 (mmm) cc_final: 0.7167 (tpp) REVERT: C 18 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7584 (tm-30) REVERT: D 97 LYS cc_start: 0.7222 (tmtt) cc_final: 0.6909 (ttpt) REVERT: D 98 LEU cc_start: 0.7570 (mt) cc_final: 0.7281 (mp) REVERT: D 117 LEU cc_start: 0.6823 (mm) cc_final: 0.6593 (mt) outliers start: 24 outliers final: 19 residues processed: 184 average time/residue: 0.2423 time to fit residues: 61.3443 Evaluate side-chains 185 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 158 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 892 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.139671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108130 restraints weight = 10495.826| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.76 r_work: 0.3066 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8833 Z= 0.191 Angle : 0.487 8.377 11998 Z= 0.262 Chirality : 0.041 0.153 1356 Planarity : 0.003 0.036 1537 Dihedral : 4.564 54.760 1187 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.62 % Allowed : 10.79 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.26), residues: 1077 helix: 1.07 (0.24), residues: 510 sheet: 0.07 (0.49), residues: 96 loop : -0.25 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 509 HIS 0.008 0.001 HIS A 892 PHE 0.014 0.001 PHE A 340 TYR 0.017 0.001 TYR A 867 ARG 0.009 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 ASN cc_start: 0.6957 (t0) cc_final: 0.6383 (p0) REVERT: A 515 TYR cc_start: 0.8934 (m-80) cc_final: 0.8467 (m-80) REVERT: A 633 MET cc_start: 0.8838 (tmm) cc_final: 0.8498 (ttp) REVERT: A 703 ASN cc_start: 0.8843 (m-40) cc_final: 0.8520 (m110) REVERT: A 743 ASP cc_start: 0.8741 (m-30) cc_final: 0.8477 (m-30) REVERT: C 3 MET cc_start: 0.7532 (mmm) cc_final: 0.7281 (tpp) REVERT: C 18 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 97 LYS cc_start: 0.7299 (tmtt) cc_final: 0.6962 (ttpt) REVERT: D 98 LEU cc_start: 0.7519 (mt) cc_final: 0.7227 (mp) REVERT: D 117 LEU cc_start: 0.6899 (mm) cc_final: 0.6665 (mt) outliers start: 25 outliers final: 20 residues processed: 185 average time/residue: 0.2373 time to fit residues: 60.4281 Evaluate side-chains 183 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 28 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111575 restraints weight = 10628.967| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.80 r_work: 0.3110 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8833 Z= 0.131 Angle : 0.457 6.119 11998 Z= 0.247 Chirality : 0.040 0.159 1356 Planarity : 0.003 0.031 1537 Dihedral : 4.327 51.641 1187 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.26 % Allowed : 12.25 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.26), residues: 1077 helix: 1.20 (0.25), residues: 511 sheet: 0.02 (0.47), residues: 113 loop : -0.06 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 29 HIS 0.005 0.001 HIS A 892 PHE 0.013 0.001 PHE A 340 TYR 0.016 0.001 TYR A 867 ARG 0.003 0.000 ARG A 735 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.8032 (m-30) cc_final: 0.7660 (t70) REVERT: A 380 MET cc_start: 0.8525 (mmt) cc_final: 0.8239 (mmt) REVERT: A 497 ASN cc_start: 0.6942 (t0) cc_final: 0.6373 (p0) REVERT: A 515 TYR cc_start: 0.8864 (m-80) cc_final: 0.8549 (m-80) REVERT: A 633 MET cc_start: 0.8876 (tmm) cc_final: 0.8513 (ttp) REVERT: A 703 ASN cc_start: 0.8766 (m-40) cc_final: 0.8429 (m110) REVERT: A 733 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6118 (mmt180) REVERT: A 743 ASP cc_start: 0.8684 (m-30) cc_final: 0.8477 (m-30) REVERT: A 887 TYR cc_start: 0.8847 (t80) cc_final: 0.8582 (t80) REVERT: C 3 MET cc_start: 0.7443 (mmm) cc_final: 0.7188 (tpp) REVERT: C 18 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 60 LEU cc_start: 0.7336 (mt) cc_final: 0.6931 (mt) REVERT: D 97 LYS cc_start: 0.7358 (tmtt) cc_final: 0.7012 (ttpt) REVERT: D 98 LEU cc_start: 0.7517 (mt) cc_final: 0.7199 (mp) REVERT: D 117 LEU cc_start: 0.6887 (mm) cc_final: 0.6642 (mt) outliers start: 12 outliers final: 11 residues processed: 177 average time/residue: 0.2424 time to fit residues: 58.2054 Evaluate side-chains 179 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110898 restraints weight = 10548.377| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.77 r_work: 0.3095 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8833 Z= 0.160 Angle : 0.475 6.021 11998 Z= 0.258 Chirality : 0.040 0.153 1356 Planarity : 0.003 0.030 1537 Dihedral : 4.316 49.738 1187 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.26 % Allowed : 13.09 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.70 (0.26), residues: 1077 helix: 1.15 (0.24), residues: 510 sheet: 0.04 (0.47), residues: 113 loop : -0.09 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 154 HIS 0.005 0.001 HIS A 892 PHE 0.013 0.001 PHE A 340 TYR 0.016 0.001 TYR A 867 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8475 (mmt) cc_final: 0.8235 (mmt) REVERT: A 497 ASN cc_start: 0.6961 (t0) cc_final: 0.6406 (p0) REVERT: A 515 TYR cc_start: 0.8882 (m-80) cc_final: 0.8469 (m-80) REVERT: A 633 MET cc_start: 0.8886 (tmm) cc_final: 0.8510 (ttp) REVERT: A 680 THR cc_start: 0.8550 (p) cc_final: 0.8338 (p) REVERT: A 703 ASN cc_start: 0.8787 (m-40) cc_final: 0.8469 (m110) REVERT: A 733 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6292 (mmt180) REVERT: A 743 ASP cc_start: 0.8671 (m-30) cc_final: 0.8450 (m-30) REVERT: A 887 TYR cc_start: 0.8849 (t80) cc_final: 0.8574 (t80) REVERT: C 3 MET cc_start: 0.7566 (mmm) cc_final: 0.7291 (tpp) REVERT: C 18 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7516 (tm-30) REVERT: C 60 LEU cc_start: 0.7324 (mt) cc_final: 0.6921 (mt) REVERT: D 97 LYS cc_start: 0.7361 (tmtt) cc_final: 0.7036 (ttpt) REVERT: D 98 LEU cc_start: 0.7482 (mt) cc_final: 0.7208 (mp) outliers start: 12 outliers final: 10 residues processed: 178 average time/residue: 0.2217 time to fit residues: 53.4049 Evaluate side-chains 177 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.0470 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 109 ASN B 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111388 restraints weight = 10484.781| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.77 r_work: 0.3104 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8833 Z= 0.147 Angle : 0.467 6.746 11998 Z= 0.253 Chirality : 0.040 0.153 1356 Planarity : 0.003 0.030 1537 Dihedral : 4.211 45.701 1187 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.26 % Allowed : 13.51 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.71 (0.26), residues: 1077 helix: 1.18 (0.24), residues: 510 sheet: -0.19 (0.46), residues: 118 loop : -0.03 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 29 HIS 0.004 0.001 HIS A 892 PHE 0.012 0.001 PHE A 340 TYR 0.017 0.001 TYR A 867 ARG 0.005 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ASP cc_start: 0.8354 (m-30) cc_final: 0.7529 (p0) REVERT: A 284 ASP cc_start: 0.8079 (m-30) cc_final: 0.7719 (t70) REVERT: A 380 MET cc_start: 0.8440 (mmt) cc_final: 0.8210 (mmt) REVERT: A 497 ASN cc_start: 0.6967 (t0) cc_final: 0.6425 (p0) REVERT: A 515 TYR cc_start: 0.8923 (m-80) cc_final: 0.8583 (m-80) REVERT: A 633 MET cc_start: 0.8892 (tmm) cc_final: 0.8516 (ttp) REVERT: A 680 THR cc_start: 0.8535 (p) cc_final: 0.8325 (p) REVERT: A 703 ASN cc_start: 0.8845 (m-40) cc_final: 0.8491 (m110) REVERT: A 733 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6413 (mmt180) REVERT: A 743 ASP cc_start: 0.8670 (m-30) cc_final: 0.8449 (m-30) REVERT: A 886 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6893 (tp-100) REVERT: C 3 MET cc_start: 0.7504 (mmm) cc_final: 0.7224 (tpp) REVERT: C 18 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 60 LEU cc_start: 0.7361 (mt) cc_final: 0.6958 (mt) REVERT: D 97 LYS cc_start: 0.7388 (tmtt) cc_final: 0.7053 (ttpt) REVERT: D 98 LEU cc_start: 0.7466 (mt) cc_final: 0.7148 (mp) outliers start: 12 outliers final: 11 residues processed: 181 average time/residue: 0.2229 time to fit residues: 54.9506 Evaluate side-chains 175 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 733 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.0020 chunk 85 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN B 109 ASN B 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.142733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111490 restraints weight = 10502.016| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.79 r_work: 0.3116 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8833 Z= 0.152 Angle : 0.482 6.010 11998 Z= 0.258 Chirality : 0.040 0.153 1356 Planarity : 0.003 0.032 1537 Dihedral : 4.162 41.918 1187 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.47 % Allowed : 13.61 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.70 (0.26), residues: 1077 helix: 1.17 (0.24), residues: 510 sheet: -0.18 (0.47), residues: 118 loop : -0.05 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 29 HIS 0.006 0.001 HIS A 892 PHE 0.012 0.001 PHE A 340 TYR 0.015 0.001 TYR A 867 ARG 0.004 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5416.97 seconds wall clock time: 95 minutes 13.22 seconds (5713.22 seconds total)