Starting phenix.real_space_refine on Tue Apr 29 12:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nur_0520/04_2025/6nur_0520.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nur_0520/04_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_0520/04_2025/6nur_0520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nur_0520/04_2025/6nur_0520.map" model { file = "/net/cci-nas-00/data/ceres_data/6nur_0520/04_2025/6nur_0520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nur_0520/04_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-5669/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: 5.22, per 1000 atoms: 0.60 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: 2.10 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 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: 1.13 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: 3.04 Time building geometry restraints manager: 2.50 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: 1.090 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.370 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- 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 : 0.020 0.742 8841 Z= 0.891 Angle : 1.611 37.377 12004 Z= 1.083 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 Details of bonding type rmsd hydrogen bonds : bond 0.16938 ( 424) hydrogen bonds : angle 7.03187 ( 1182) metal coordination : bond 0.38687 ( 8) metal coordination : angle 19.51850 ( 6) covalent geometry : bond 0.01566 ( 8833) covalent geometry : angle 1.55166 (11998) *********************** 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 : 0.865 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: 0.2436 time to fit residues: 92.7873 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 : 0.935 ------------------------------------------------------------------------------- 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 8841 Z= 0.145 Angle : 0.596 6.706 12004 Z= 0.323 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 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 424) hydrogen bonds : angle 4.82345 ( 1182) metal coordination : bond 0.01263 ( 8) metal coordination : angle 3.03065 ( 6) covalent geometry : bond 0.00308 ( 8833) covalent geometry : angle 0.59180 (11998) *********************** 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 : 0.987 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: 0.2466 time to fit residues: 66.5537 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 : 0.979 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS A 703 ASN B 179 ASN D 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108412 restraints weight = 10544.937| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.81 r_work: 0.3056 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8841 Z= 0.189 Angle : 0.588 9.061 12004 Z= 0.311 Chirality : 0.044 0.155 1356 Planarity : 0.004 0.067 1537 Dihedral : 5.134 59.558 1191 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.72 % Allowed : 8.59 % Favored : 88.69 % 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: 0.40 (0.25), residues: 1077 helix: 0.72 (0.23), residues: 514 sheet: 0.32 (0.52), residues: 98 loop : -0.11 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 509 HIS 0.006 0.002 HIS A 439 PHE 0.017 0.002 PHE A 165 TYR 0.025 0.002 TYR A 867 ARG 0.003 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 424) hydrogen bonds : angle 4.46609 ( 1182) metal coordination : bond 0.01095 ( 8) metal coordination : angle 2.88397 ( 6) covalent geometry : bond 0.00441 ( 8833) covalent geometry : angle 0.58442 (11998) *********************** 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 197 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8879 (mt) REVERT: A 497 ASN cc_start: 0.6960 (t0) cc_final: 0.6156 (p0) REVERT: A 589 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (mm) REVERT: A 631 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8408 (tmt170) REVERT: A 633 MET cc_start: 0.8814 (tmm) cc_final: 0.8551 (ttp) REVERT: A 681 SER cc_start: 0.8519 (t) cc_final: 0.8222 (p) REVERT: A 743 ASP cc_start: 0.8716 (m-30) cc_final: 0.8397 (m-30) REVERT: A 918 GLU cc_start: 0.8700 (tt0) cc_final: 0.8453 (tt0) REVERT: B 158 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: D 94 MET cc_start: 0.7959 (mtp) cc_final: 0.7748 (mtp) REVERT: D 98 LEU cc_start: 0.8010 (mp) cc_final: 0.7757 (mp) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.2295 time to fit residues: 58.3880 Evaluate side-chains 186 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 221 ASP 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 589 ILE 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 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: 1.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 chunk 9 optimal weight: 4.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- 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 B 109 ASN D 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108083 restraints weight = 10521.169| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.81 r_work: 0.3059 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8841 Z= 0.146 Angle : 0.527 8.007 12004 Z= 0.276 Chirality : 0.042 0.146 1356 Planarity : 0.004 0.047 1537 Dihedral : 5.008 57.067 1191 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.62 % Allowed : 8.38 % Favored : 89.01 % 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 (0.26), residues: 1077 helix: 0.88 (0.24), residues: 514 sheet: 0.08 (0.50), residues: 99 loop : -0.14 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 509 HIS 0.005 0.001 HIS A 439 PHE 0.015 0.002 PHE A 881 TYR 0.020 0.002 TYR A 867 ARG 0.007 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 424) hydrogen bonds : angle 4.26986 ( 1182) metal coordination : bond 0.00887 ( 8) metal coordination : angle 1.85762 ( 6) covalent geometry : bond 0.00342 ( 8833) covalent geometry : angle 0.52533 (11998) *********************** 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 195 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8608 (mt) REVERT: A 497 ASN cc_start: 0.7077 (t0) cc_final: 0.6287 (p0) REVERT: A 633 MET cc_start: 0.8844 (tmm) cc_final: 0.8544 (ttp) REVERT: A 681 SER cc_start: 0.8657 (t) cc_final: 0.8427 (p) REVERT: A 703 ASN cc_start: 0.8841 (m-40) cc_final: 0.8604 (m110) REVERT: A 743 ASP cc_start: 0.8725 (m-30) cc_final: 0.8405 (m-30) REVERT: A 918 GLU cc_start: 0.8721 (tt0) cc_final: 0.8482 (tt0) REVERT: B 158 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: D 98 LEU cc_start: 0.7857 (mp) cc_final: 0.7632 (mp) outliers start: 25 outliers final: 19 residues processed: 187 average time/residue: 0.2452 time to fit residues: 60.8759 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 : 0.901 ------------------------------------------------------------------------------- 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 281 CYS Chi-restraints excluded: chain A residue 330 VAL 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 536 ILE Chi-restraints excluded: chain A residue 615 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 96 optimal weight: 0.0970 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 66 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 224 GLN A 360 ASN A 791 ASN B 109 ASN D 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110174 restraints weight = 10488.397| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.81 r_work: 0.3092 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8841 Z= 0.111 Angle : 0.486 7.284 12004 Z= 0.256 Chirality : 0.040 0.157 1356 Planarity : 0.003 0.037 1537 Dihedral : 4.636 57.258 1187 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.30 % Allowed : 9.32 % Favored : 88.38 % 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: 0.63 (0.26), residues: 1077 helix: 1.09 (0.24), residues: 507 sheet: -0.07 (0.46), residues: 117 loop : -0.10 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 509 HIS 0.006 0.001 HIS A 892 PHE 0.011 0.001 PHE A 881 TYR 0.015 0.001 TYR A 867 ARG 0.003 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 424) hydrogen bonds : angle 4.08370 ( 1182) metal coordination : bond 0.00657 ( 8) metal coordination : angle 1.54672 ( 6) covalent geometry : bond 0.00251 ( 8833) covalent geometry : angle 0.48501 (11998) *********************** 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 193 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7070 (t0) cc_final: 0.6332 (p0) REVERT: A 515 TYR cc_start: 0.8892 (m-80) cc_final: 0.8532 (m-80) REVERT: A 633 MET cc_start: 0.8846 (tmm) cc_final: 0.8519 (ttp) REVERT: A 703 ASN cc_start: 0.8832 (m-40) cc_final: 0.8548 (m110) REVERT: A 743 ASP cc_start: 0.8693 (m-30) cc_final: 0.8451 (m-30) REVERT: A 825 ASP cc_start: 0.7229 (t0) cc_final: 0.6821 (p0) REVERT: A 918 GLU cc_start: 0.8702 (tt0) cc_final: 0.8471 (tt0) REVERT: B 158 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: D 98 LEU cc_start: 0.7643 (mt) cc_final: 0.7395 (mp) outliers start: 22 outliers final: 17 residues processed: 183 average time/residue: 0.3253 time to fit residues: 79.6907 Evaluate side-chains 182 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 451 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS 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 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 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: 1.9990 chunk 104 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 439 HIS B 109 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 = 0.3548 r_free = 0.3548 target = 0.140177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108317 restraints weight = 10323.547| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.78 r_work: 0.3080 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8841 Z= 0.142 Angle : 0.504 7.515 12004 Z= 0.268 Chirality : 0.042 0.164 1356 Planarity : 0.004 0.046 1537 Dihedral : 4.645 56.165 1187 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.41 % Allowed : 10.16 % Favored : 87.43 % 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: 0.58 (0.26), residues: 1077 helix: 1.08 (0.24), residues: 504 sheet: 0.07 (0.50), residues: 96 loop : -0.20 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.005 0.001 HIS A 572 PHE 0.013 0.002 PHE A 881 TYR 0.016 0.002 TYR A 788 ARG 0.009 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 424) hydrogen bonds : angle 4.10295 ( 1182) metal coordination : bond 0.00769 ( 8) metal coordination : angle 1.54498 ( 6) covalent geometry : bond 0.00338 ( 8833) covalent geometry : angle 0.50333 (11998) *********************** 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 192 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7162 (t0) cc_final: 0.6389 (p0) REVERT: A 515 TYR cc_start: 0.8924 (m-80) cc_final: 0.8577 (m-80) REVERT: A 566 MET cc_start: 0.8945 (mtp) cc_final: 0.8682 (mtp) REVERT: A 633 MET cc_start: 0.8818 (tmm) cc_final: 0.8484 (ttp) REVERT: A 703 ASN cc_start: 0.8854 (m-40) cc_final: 0.8537 (m110) REVERT: A 743 ASP cc_start: 0.8706 (m-30) cc_final: 0.8419 (m-30) REVERT: A 825 ASP cc_start: 0.7236 (t0) cc_final: 0.6872 (p0) REVERT: A 918 GLU cc_start: 0.8734 (tt0) cc_final: 0.8485 (tt0) REVERT: B 158 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: C 18 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7558 (tm-30) outliers start: 23 outliers final: 21 residues processed: 186 average time/residue: 0.2580 time to fit residues: 64.4813 Evaluate side-chains 184 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 451 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 615 MET 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 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: 7.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 0.0270 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109554 restraints weight = 10490.890| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.78 r_work: 0.3078 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8841 Z= 0.115 Angle : 0.505 11.385 12004 Z= 0.265 Chirality : 0.041 0.157 1356 Planarity : 0.003 0.036 1537 Dihedral : 4.572 55.657 1187 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.20 % Allowed : 10.47 % Favored : 87.33 % 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: 0.61 (0.26), residues: 1077 helix: 1.05 (0.24), residues: 508 sheet: 0.06 (0.50), residues: 96 loop : -0.11 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 509 HIS 0.009 0.001 HIS A 892 PHE 0.011 0.001 PHE A 881 TYR 0.017 0.001 TYR A 867 ARG 0.009 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 424) hydrogen bonds : angle 4.10926 ( 1182) metal coordination : bond 0.00622 ( 8) metal coordination : angle 1.27025 ( 6) covalent geometry : bond 0.00267 ( 8833) covalent geometry : angle 0.50412 (11998) *********************** 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 185 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7046 (t0) cc_final: 0.6337 (p0) REVERT: A 515 TYR cc_start: 0.8882 (m-80) cc_final: 0.8620 (m-80) REVERT: A 633 MET cc_start: 0.8816 (tmm) cc_final: 0.8467 (ttp) REVERT: A 703 ASN cc_start: 0.8793 (m-40) cc_final: 0.8460 (m110) REVERT: A 743 ASP cc_start: 0.8708 (m-30) cc_final: 0.8447 (m-30) REVERT: A 750 ARG cc_start: 0.8324 (mtp180) cc_final: 0.8072 (mtp180) REVERT: A 825 ASP cc_start: 0.7254 (t0) cc_final: 0.6953 (p0) REVERT: A 886 GLN cc_start: 0.7852 (mp10) cc_final: 0.7508 (mp10) REVERT: A 918 GLU cc_start: 0.8704 (tt0) cc_final: 0.8483 (tt0) REVERT: C 10 SER cc_start: 0.7349 (m) cc_final: 0.7011 (p) REVERT: C 18 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7628 (tm-30) outliers start: 21 outliers final: 14 residues processed: 178 average time/residue: 0.2906 time to fit residues: 70.5879 Evaluate side-chains 178 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 451 SER 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 856 ILE Chi-restraints excluded: chain A residue 883 LEU 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: 0.6980 chunk 20 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN D 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.111444 restraints weight = 10635.036| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.80 r_work: 0.3103 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8841 Z= 0.102 Angle : 0.489 12.382 12004 Z= 0.258 Chirality : 0.040 0.150 1356 Planarity : 0.003 0.033 1537 Dihedral : 4.455 56.596 1187 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.68 % Allowed : 11.20 % Favored : 87.12 % 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: 0.68 (0.26), residues: 1077 helix: 1.11 (0.24), residues: 509 sheet: -0.03 (0.46), residues: 113 loop : -0.05 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 154 HIS 0.005 0.001 HIS A 892 PHE 0.010 0.001 PHE A 881 TYR 0.014 0.001 TYR A 867 ARG 0.008 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 424) hydrogen bonds : angle 4.02009 ( 1182) metal coordination : bond 0.00494 ( 8) metal coordination : angle 1.10905 ( 6) covalent geometry : bond 0.00232 ( 8833) covalent geometry : angle 0.48882 (11998) *********************** 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 187 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.7065 (t0) cc_final: 0.6359 (p0) REVERT: A 515 TYR cc_start: 0.8883 (m-80) cc_final: 0.8469 (m-80) REVERT: A 633 MET cc_start: 0.8841 (tmm) cc_final: 0.8465 (ttp) REVERT: A 703 ASN cc_start: 0.8791 (m-40) cc_final: 0.8464 (m110) REVERT: A 743 ASP cc_start: 0.8674 (m-30) cc_final: 0.8448 (m-30) REVERT: A 750 ARG cc_start: 0.8316 (mtp180) cc_final: 0.8054 (mtp180) REVERT: A 825 ASP cc_start: 0.7366 (t0) cc_final: 0.7021 (p0) REVERT: A 836 ARG cc_start: 0.7833 (ttp-110) cc_final: 0.7357 (ttm-80) REVERT: A 886 GLN cc_start: 0.7565 (mp10) cc_final: 0.7206 (mp10) REVERT: A 918 GLU cc_start: 0.8703 (tt0) cc_final: 0.8480 (tt0) REVERT: C 18 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7619 (tm-30) outliers start: 16 outliers final: 15 residues processed: 182 average time/residue: 0.2906 time to fit residues: 71.7179 Evaluate side-chains 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 372 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 790 ASN C 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108662 restraints weight = 10579.018| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.77 r_work: 0.3063 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8841 Z= 0.147 Angle : 0.524 12.138 12004 Z= 0.279 Chirality : 0.042 0.162 1356 Planarity : 0.004 0.037 1537 Dihedral : 4.532 55.633 1187 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.57 % Allowed : 11.62 % Favored : 86.81 % 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: 0.57 (0.26), residues: 1077 helix: 1.03 (0.24), residues: 508 sheet: 0.08 (0.51), residues: 94 loop : -0.16 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 216 HIS 0.006 0.001 HIS A 892 PHE 0.015 0.002 PHE A 340 TYR 0.016 0.002 TYR A 867 ARG 0.008 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 424) hydrogen bonds : angle 4.17127 ( 1182) metal coordination : bond 0.00736 ( 8) metal coordination : angle 1.28173 ( 6) covalent geometry : bond 0.00351 ( 8833) covalent geometry : angle 0.52371 (11998) *********************** 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 185 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.6917 (t0) cc_final: 0.6291 (p0) REVERT: A 515 TYR cc_start: 0.8932 (m-80) cc_final: 0.8570 (m-80) REVERT: A 633 MET cc_start: 0.8870 (tmm) cc_final: 0.8513 (ttp) REVERT: A 680 THR cc_start: 0.8598 (p) cc_final: 0.8370 (p) REVERT: A 703 ASN cc_start: 0.8910 (m-40) cc_final: 0.8582 (m110) REVERT: A 743 ASP cc_start: 0.8697 (m-30) cc_final: 0.8407 (m-30) REVERT: A 750 ARG cc_start: 0.8346 (mtp180) cc_final: 0.8100 (mtp180) REVERT: A 886 GLN cc_start: 0.7585 (mp10) cc_final: 0.7314 (mp10) REVERT: A 918 GLU cc_start: 0.8740 (tt0) cc_final: 0.8531 (tt0) REVERT: C 18 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 15 outliers final: 15 residues processed: 183 average time/residue: 0.2714 time to fit residues: 67.8430 Evaluate side-chains 180 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.110464 restraints weight = 10489.235| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.76 r_work: 0.3096 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8841 Z= 0.110 Angle : 0.504 12.414 12004 Z= 0.267 Chirality : 0.041 0.151 1356 Planarity : 0.003 0.033 1537 Dihedral : 4.488 56.110 1187 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.68 % Allowed : 12.04 % Favored : 86.28 % 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: 0.64 (0.26), residues: 1077 helix: 1.10 (0.24), residues: 508 sheet: 0.19 (0.48), residues: 104 loop : -0.15 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 216 HIS 0.005 0.001 HIS A 892 PHE 0.013 0.001 PHE A 859 TYR 0.017 0.001 TYR A 867 ARG 0.008 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 424) hydrogen bonds : angle 4.05452 ( 1182) metal coordination : bond 0.00565 ( 8) metal coordination : angle 1.12470 ( 6) covalent geometry : bond 0.00252 ( 8833) covalent geometry : angle 0.50382 (11998) ********************** 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 181 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 497 ASN cc_start: 0.6955 (t0) cc_final: 0.6363 (p0) REVERT: A 515 TYR cc_start: 0.8897 (m-80) cc_final: 0.8521 (m-80) REVERT: A 633 MET cc_start: 0.8831 (tmm) cc_final: 0.8471 (ttp) REVERT: A 680 THR cc_start: 0.8571 (p) cc_final: 0.8360 (p) REVERT: A 703 ASN cc_start: 0.8795 (m-40) cc_final: 0.8455 (m110) REVERT: A 743 ASP cc_start: 0.8692 (m-30) cc_final: 0.8431 (m-30) REVERT: A 750 ARG cc_start: 0.8311 (mtp180) cc_final: 0.8037 (mtp180) REVERT: A 794 MET cc_start: 0.8353 (ttp) cc_final: 0.8110 (ttp) REVERT: A 918 GLU cc_start: 0.8692 (tt0) cc_final: 0.8458 (tt0) REVERT: C 18 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 16 outliers final: 15 residues processed: 177 average time/residue: 0.2317 time to fit residues: 55.1467 Evaluate side-chains 178 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 365 ARG Chi-restraints excluded: chain A residue 451 SER 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 820 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 100 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111158 restraints weight = 10458.015| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.75 r_work: 0.3091 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8841 Z= 0.111 Angle : 0.510 12.322 12004 Z= 0.271 Chirality : 0.041 0.210 1356 Planarity : 0.003 0.033 1537 Dihedral : 4.439 56.776 1187 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.78 % Allowed : 12.25 % Favored : 85.97 % 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: 0.61 (0.26), residues: 1077 helix: 1.09 (0.24), residues: 509 sheet: -0.15 (0.47), residues: 115 loop : -0.10 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 509 HIS 0.004 0.001 HIS A 892 PHE 0.013 0.001 PHE A 859 TYR 0.017 0.001 TYR A 867 ARG 0.008 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03267 ( 424) hydrogen bonds : angle 4.08395 ( 1182) metal coordination : bond 0.00520 ( 8) metal coordination : angle 1.07276 ( 6) covalent geometry : bond 0.00251 ( 8833) covalent geometry : angle 0.50966 (11998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.76 seconds wall clock time: 98 minutes 53.35 seconds (5933.35 seconds total)