Starting phenix.real_space_refine on Wed Sep 17 09:27:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.cif Found real_map, /net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.map" model { file = "/net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6npy_0476/09_2025/6npy_0476.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 P 2 5.49 5 S 70 5.16 5 C 4823 2.51 5 N 1286 2.21 5 O 1405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7586 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6192 Classifications: {'peptide': 798} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 25, 'TRANS': 772} Chain breaks: 7 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 3, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 1367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1385 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 284 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 284 " occ=0.50 Time building chain proxies: 2.04, per 1000 atoms: 0.27 Number of scatterers: 7586 At special positions: 0 Unit cell: (115.08, 89.88, 100.8, 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) S 70 16.00 P 2 15.00 O 1405 8.00 N 1286 7.00 C 4823 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: 0.45 Conformation dependent library (CDL) restraints added in 428.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 49.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.638A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.796A pdb=" N ARG A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.873A pdb=" N LEU A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 384 removed outlier: 3.600A pdb=" N PHE A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.757A pdb=" N SER A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.661A pdb=" N CYS A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.883A pdb=" N VAL A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 472 removed outlier: 4.042A pdb=" N TRP A 465 " --> pdb=" O CYS A 461 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA A 472 " --> pdb=" O CYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.977A pdb=" N SER A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 521 through 535 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 562 through 577 removed outlier: 3.706A pdb=" N ILE A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.782A pdb=" N GLU A 585 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 586 " --> pdb=" O ASN A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 586' Processing helix chain 'A' and resid 617 through 634 Proline residue: A 623 - end of helix removed outlier: 4.428A pdb=" N GLU A 634 " --> pdb=" O TYR A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.772A pdb=" N ALA A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 removed outlier: 5.093A pdb=" N VAL A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 removed outlier: 3.985A pdb=" N ARG A 757 " --> pdb=" O ASP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 783 through 794 removed outlier: 4.601A pdb=" N ASP A 787 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.892A pdb=" N LEU A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 852 removed outlier: 4.264A pdb=" N SER A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 894 through 909 removed outlier: 3.548A pdb=" N CYS A 898 " --> pdb=" O LEU A 894 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 935 removed outlier: 3.707A pdb=" N ILE A 927 " --> pdb=" O GLY A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 966 Processing helix chain 'A' and resid 979 through 993 removed outlier: 3.732A pdb=" N GLY A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 993 " --> pdb=" O GLU A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.871A pdb=" N LYS A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.886A pdb=" N PHE B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 155 removed outlier: 4.202A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 214 through 232 removed outlier: 3.596A pdb=" N ASP B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.561A pdb=" N CYS B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 284 through 298 removed outlier: 4.170A pdb=" N ASP B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.913A pdb=" N THR A 219 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 366 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 221 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE A 368 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN A 223 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 220 " --> pdb=" O ILE A 346 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR A 348 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 222 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 343 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 345 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 299 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 744 through 745 removed outlier: 7.123A pdb=" N LEU A 744 " --> pdb=" O TRP A 774 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLY A 776 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 804 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 801 " --> pdb=" O TRP A 831 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 915 through 916 removed outlier: 6.923A pdb=" N LEU A 915 " --> pdb=" O GLU A 945 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.740A pdb=" N GLY B 117 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 169 " --> pdb=" O GLY B 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 265 hydrogen bonds defined for protein. 756 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: 1.03 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2435 1.34 - 1.46: 1641 1.46 - 1.58: 3564 1.58 - 1.70: 3 1.70 - 1.82: 96 Bond restraints: 7739 Sorted by residual: bond pdb=" C MET A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.18e+01 bond pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.54e-02 4.22e+03 2.93e+00 bond pdb=" C LYS A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.82e+00 bond pdb=" CB TRP A 831 " pdb=" CG TRP A 831 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.54e+00 bond pdb=" CA LEU A 746 " pdb=" CB LEU A 746 " ideal model delta sigma weight residual 1.531 1.480 0.051 3.28e-02 9.30e+02 2.39e+00 ... (remaining 7734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9814 2.10 - 4.20: 508 4.20 - 6.29: 93 6.29 - 8.39: 35 8.39 - 10.49: 13 Bond angle restraints: 10463 Sorted by residual: angle pdb=" N VAL A 860 " pdb=" CA VAL A 860 " pdb=" C VAL A 860 " ideal model delta sigma weight residual 111.77 105.80 5.97 1.04e+00 9.25e-01 3.30e+01 angle pdb=" C GLN A 432 " pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 122.46 129.31 -6.85 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N ILE A 475 " pdb=" CA ILE A 475 " pdb=" C ILE A 475 " ideal model delta sigma weight residual 113.71 109.13 4.58 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C VAL A 262 " pdb=" N SER A 263 " pdb=" CA SER A 263 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N LEU A 551 " pdb=" CA LEU A 551 " pdb=" C LEU A 551 " ideal model delta sigma weight residual 109.81 118.79 -8.98 2.21e+00 2.05e-01 1.65e+01 ... (remaining 10458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4019 17.56 - 35.13: 530 35.13 - 52.69: 93 52.69 - 70.25: 14 70.25 - 87.81: 15 Dihedral angle restraints: 4671 sinusoidal: 1853 harmonic: 2818 Sorted by residual: dihedral pdb=" CA VAL A 860 " pdb=" C VAL A 860 " pdb=" N GLY A 861 " pdb=" CA GLY A 861 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA CYS A 784 " pdb=" C CYS A 784 " pdb=" N CYS A 785 " pdb=" CA CYS A 785 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO A 363 " pdb=" C PRO A 363 " pdb=" N ARG A 364 " pdb=" CA ARG A 364 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 944 0.073 - 0.146: 202 0.146 - 0.218: 30 0.218 - 0.291: 4 0.291 - 0.364: 3 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CB ILE A 480 " pdb=" CA ILE A 480 " pdb=" CG1 ILE A 480 " pdb=" CG2 ILE A 480 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 860 " pdb=" CA VAL A 860 " pdb=" CG1 VAL A 860 " pdb=" CG2 VAL A 860 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1180 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " -0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 284 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 648 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 649 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 649 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 649 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.028 2.00e-02 2.50e+03 2.08e-02 7.57e+00 pdb=" CG PHE A 648 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " 0.002 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1643 2.77 - 3.31: 7334 3.31 - 3.84: 12697 3.84 - 4.37: 14205 4.37 - 4.90: 23142 Nonbonded interactions: 59021 Sorted by model distance: nonbonded pdb=" O MET B 295 " pdb=" OG1 THR B 299 " model vdw 2.244 3.040 nonbonded pdb=" O SER A1014 " pdb=" OG1 THR A1018 " model vdw 2.251 3.040 nonbonded pdb=" O PRO B 134 " pdb=" OG1 THR B 137 " model vdw 2.254 3.040 nonbonded pdb=" O LEU A 706 " pdb=" OG SER A 709 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 570 " pdb=" O GLU A 585 " model vdw 2.278 3.040 ... (remaining 59016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.130 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.006 0.061 7739 Z= 0.301 Angle : 1.160 10.488 10463 Z= 0.608 Chirality : 0.063 0.364 1183 Planarity : 0.007 0.094 1327 Dihedral : 16.443 87.813 2841 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.63 % Favored : 85.26 % Rotamer: Outliers : 0.84 % Allowed : 13.58 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.90 (0.22), residues: 946 helix: -3.04 (0.17), residues: 402 sheet: -3.72 (0.52), residues: 74 loop : -3.36 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 121 TYR 0.029 0.003 TYR A 531 PHE 0.045 0.003 PHE A 648 TRP 0.011 0.002 TRP A 241 HIS 0.011 0.002 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00636 ( 7739) covalent geometry : angle 1.16035 (10463) hydrogen bonds : bond 0.17440 ( 265) hydrogen bonds : angle 7.93270 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 TRP cc_start: 0.6672 (t60) cc_final: 0.6468 (t60) REVERT: A 254 LEU cc_start: 0.8144 (mt) cc_final: 0.7501 (mt) REVERT: A 302 PHE cc_start: 0.7308 (t80) cc_final: 0.7015 (t80) REVERT: A 567 GLU cc_start: 0.8336 (pp20) cc_final: 0.7432 (pp20) REVERT: A 571 LEU cc_start: 0.7718 (mt) cc_final: 0.6619 (mt) REVERT: A 630 TYR cc_start: 0.8223 (m-80) cc_final: 0.7946 (m-80) REVERT: A 685 MET cc_start: 0.8512 (tpt) cc_final: 0.8226 (tpt) REVERT: A 701 MET cc_start: 0.5707 (mmt) cc_final: 0.5429 (mmm) REVERT: A 782 HIS cc_start: 0.7189 (t70) cc_final: 0.6344 (t-90) REVERT: B 162 ILE cc_start: 0.7270 (mp) cc_final: 0.6215 (mp) REVERT: B 163 LYS cc_start: 0.7561 (mmtm) cc_final: 0.6747 (pttp) outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.1137 time to fit residues: 24.8158 Evaluate side-chains 132 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 895 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN A 782 HIS A 909 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.084087 restraints weight = 44110.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.087112 restraints weight = 22461.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.089060 restraints weight = 14538.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090358 restraints weight = 10861.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.091164 restraints weight = 8861.348| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3870 r_free = 0.3870 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7739 Z= 0.183 Angle : 0.843 9.961 10463 Z= 0.422 Chirality : 0.046 0.248 1183 Planarity : 0.006 0.078 1327 Dihedral : 8.289 56.389 1048 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 3.85 % Allowed : 19.95 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.24), residues: 946 helix: -1.67 (0.22), residues: 419 sheet: -3.56 (0.49), residues: 79 loop : -3.09 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 121 TYR 0.021 0.002 TYR A 570 PHE 0.021 0.002 PHE A 648 TRP 0.012 0.001 TRP A 957 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7739) covalent geometry : angle 0.84274 (10463) hydrogen bonds : bond 0.04234 ( 265) hydrogen bonds : angle 5.86166 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7887 (m90) cc_final: 0.7636 (m90) REVERT: A 630 TYR cc_start: 0.8778 (m-80) cc_final: 0.8304 (m-80) REVERT: A 701 MET cc_start: 0.5897 (mmt) cc_final: 0.5542 (mmm) REVERT: B 162 ILE cc_start: 0.7472 (mp) cc_final: 0.6777 (mp) REVERT: B 163 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7477 (mmtt) REVERT: B 207 ARG cc_start: 0.7049 (tpt170) cc_final: 0.6822 (mmm160) REVERT: B 241 MET cc_start: 0.5853 (ppp) cc_final: 0.5426 (ppp) outliers start: 32 outliers final: 23 residues processed: 158 average time/residue: 0.0863 time to fit residues: 18.4526 Evaluate side-chains 143 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 468 CYS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 GLN B 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.105924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.084854 restraints weight = 64049.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088682 restraints weight = 27613.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.091025 restraints weight = 16547.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.092538 restraints weight = 11728.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.093515 restraints weight = 9281.211| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7739 Z= 0.125 Angle : 0.783 9.291 10463 Z= 0.384 Chirality : 0.046 0.252 1183 Planarity : 0.005 0.073 1327 Dihedral : 7.749 59.579 1048 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 4.69 % Allowed : 20.91 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.26), residues: 946 helix: -1.08 (0.24), residues: 411 sheet: -3.25 (0.50), residues: 79 loop : -2.84 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 121 TYR 0.016 0.002 TYR A 570 PHE 0.016 0.001 PHE A 786 TRP 0.016 0.002 TRP A 957 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7739) covalent geometry : angle 0.78256 (10463) hydrogen bonds : bond 0.03510 ( 265) hydrogen bonds : angle 5.57209 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7850 (m90) cc_final: 0.7600 (m90) REVERT: A 521 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7364 (ptt) REVERT: A 701 MET cc_start: 0.5751 (mmt) cc_final: 0.5398 (mmm) REVERT: B 141 TYR cc_start: 0.8686 (m-80) cc_final: 0.8453 (m-80) REVERT: B 162 ILE cc_start: 0.7261 (mp) cc_final: 0.6529 (mp) REVERT: B 163 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7278 (mmtt) REVERT: B 265 GLU cc_start: 0.7056 (tp30) cc_final: 0.6421 (tt0) outliers start: 39 outliers final: 22 residues processed: 170 average time/residue: 0.0864 time to fit residues: 19.7285 Evaluate side-chains 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.105356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.084864 restraints weight = 57276.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.088395 restraints weight = 26393.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.090603 restraints weight = 16075.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.092024 restraints weight = 11643.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.092960 restraints weight = 9397.520| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3911 r_free = 0.3911 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7739 Z= 0.132 Angle : 0.777 10.073 10463 Z= 0.379 Chirality : 0.046 0.287 1183 Planarity : 0.005 0.083 1327 Dihedral : 7.562 56.979 1048 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 4.57 % Allowed : 22.36 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.26), residues: 946 helix: -0.73 (0.25), residues: 404 sheet: -3.21 (0.49), residues: 81 loop : -2.67 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.011 0.001 TYR A 570 PHE 0.017 0.001 PHE A 648 TRP 0.020 0.002 TRP A 957 HIS 0.003 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7739) covalent geometry : angle 0.77742 (10463) hydrogen bonds : bond 0.03353 ( 265) hydrogen bonds : angle 5.39349 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7810 (m90) cc_final: 0.7561 (m90) REVERT: A 521 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7340 (ptt) REVERT: A 701 MET cc_start: 0.5776 (mmt) cc_final: 0.5400 (mmm) REVERT: A 811 PHE cc_start: 0.7530 (t80) cc_final: 0.7329 (t80) REVERT: B 141 TYR cc_start: 0.8712 (m-80) cc_final: 0.8511 (m-80) REVERT: B 162 ILE cc_start: 0.7318 (mp) cc_final: 0.6619 (mp) REVERT: B 163 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7324 (mmtt) REVERT: B 265 GLU cc_start: 0.7018 (tp30) cc_final: 0.6531 (tt0) outliers start: 38 outliers final: 27 residues processed: 158 average time/residue: 0.0829 time to fit residues: 18.0522 Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.104352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.084022 restraints weight = 56906.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.087459 restraints weight = 25924.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.089626 restraints weight = 15956.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.091013 restraints weight = 11535.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.091909 restraints weight = 9238.169| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7739 Z= 0.156 Angle : 0.793 11.326 10463 Z= 0.389 Chirality : 0.046 0.233 1183 Planarity : 0.005 0.078 1327 Dihedral : 7.507 54.121 1048 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.81 % Allowed : 23.32 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.27), residues: 946 helix: -0.53 (0.26), residues: 406 sheet: -3.25 (0.49), residues: 81 loop : -2.61 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.013 0.002 TYR B 213 PHE 0.020 0.002 PHE A 648 TRP 0.023 0.002 TRP A 957 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7739) covalent geometry : angle 0.79255 (10463) hydrogen bonds : bond 0.03361 ( 265) hydrogen bonds : angle 5.39005 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7353 (ptt) REVERT: A 568 LYS cc_start: 0.8160 (tptp) cc_final: 0.7670 (tptp) REVERT: A 701 MET cc_start: 0.5845 (mmt) cc_final: 0.5471 (mmm) REVERT: B 141 TYR cc_start: 0.8704 (m-80) cc_final: 0.8477 (m-80) REVERT: B 162 ILE cc_start: 0.7279 (mp) cc_final: 0.6583 (mp) REVERT: B 163 LYS cc_start: 0.7701 (mmtm) cc_final: 0.7402 (mmtt) outliers start: 40 outliers final: 30 residues processed: 156 average time/residue: 0.0860 time to fit residues: 18.4872 Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 637 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 43 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.106510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085594 restraints weight = 58805.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.089235 restraints weight = 26562.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.091511 restraints weight = 16221.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.092993 restraints weight = 11681.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.093945 restraints weight = 9359.140| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7739 Z= 0.120 Angle : 0.770 10.986 10463 Z= 0.373 Chirality : 0.046 0.220 1183 Planarity : 0.005 0.072 1327 Dihedral : 7.256 55.751 1048 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.21 % Allowed : 24.64 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.27), residues: 946 helix: -0.41 (0.26), residues: 407 sheet: -3.02 (0.51), residues: 81 loop : -2.57 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 488 TYR 0.033 0.002 TYR A 633 PHE 0.023 0.001 PHE B 142 TRP 0.023 0.002 TRP A 957 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7739) covalent geometry : angle 0.76999 (10463) hydrogen bonds : bond 0.03168 ( 265) hydrogen bonds : angle 5.23101 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7817 (m90) cc_final: 0.6957 (t-170) REVERT: A 521 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7376 (ptt) REVERT: A 568 LYS cc_start: 0.8105 (tptp) cc_final: 0.7693 (tptp) REVERT: A 630 TYR cc_start: 0.8817 (m-80) cc_final: 0.8434 (m-80) REVERT: A 701 MET cc_start: 0.5761 (mmt) cc_final: 0.5385 (mmm) REVERT: A 790 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9043 (mm) REVERT: A 915 LEU cc_start: 0.8594 (tp) cc_final: 0.8210 (tt) REVERT: B 141 TYR cc_start: 0.8721 (m-80) cc_final: 0.8169 (m-80) REVERT: B 162 ILE cc_start: 0.7171 (mp) cc_final: 0.6502 (mp) REVERT: B 163 LYS cc_start: 0.7562 (mmtm) cc_final: 0.7241 (mmtt) outliers start: 35 outliers final: 28 residues processed: 163 average time/residue: 0.0856 time to fit residues: 19.2819 Evaluate side-chains 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN B 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.107480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.086650 restraints weight = 55837.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.090232 restraints weight = 25866.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.092515 restraints weight = 15835.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.093960 restraints weight = 11426.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.094989 restraints weight = 9139.518| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7739 Z= 0.122 Angle : 0.770 10.962 10463 Z= 0.371 Chirality : 0.045 0.202 1183 Planarity : 0.005 0.068 1327 Dihedral : 6.619 48.578 1045 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.49 % Allowed : 26.68 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.27), residues: 946 helix: -0.34 (0.26), residues: 406 sheet: -2.84 (0.54), residues: 81 loop : -2.53 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.024 0.001 TYR A 633 PHE 0.018 0.001 PHE A 811 TRP 0.026 0.002 TRP A 957 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7739) covalent geometry : angle 0.76961 (10463) hydrogen bonds : bond 0.03027 ( 265) hydrogen bonds : angle 5.17044 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7837 (m90) cc_final: 0.6938 (t-170) REVERT: A 357 GLN cc_start: 0.7741 (tp40) cc_final: 0.7498 (tt0) REVERT: A 521 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7256 (ptt) REVERT: A 568 LYS cc_start: 0.8069 (tptp) cc_final: 0.7862 (tptp) REVERT: A 688 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7289 (pp20) REVERT: A 701 MET cc_start: 0.5657 (mmt) cc_final: 0.5239 (mmm) REVERT: A 756 MET cc_start: 0.6893 (ptp) cc_final: 0.6597 (ptp) REVERT: A 790 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9073 (mm) REVERT: A 872 ILE cc_start: 0.8912 (mp) cc_final: 0.8525 (tp) REVERT: A 915 LEU cc_start: 0.8667 (tp) cc_final: 0.8364 (tt) REVERT: B 141 TYR cc_start: 0.8745 (m-80) cc_final: 0.8200 (m-80) REVERT: B 162 ILE cc_start: 0.7130 (mp) cc_final: 0.6462 (mp) REVERT: B 163 LYS cc_start: 0.7512 (mmtm) cc_final: 0.7193 (mmtt) outliers start: 29 outliers final: 23 residues processed: 162 average time/residue: 0.0822 time to fit residues: 18.5242 Evaluate side-chains 158 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.107187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085373 restraints weight = 73458.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.089357 restraints weight = 30468.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.091883 restraints weight = 17879.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.093464 restraints weight = 12521.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.094532 restraints weight = 9845.960| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7739 Z= 0.126 Angle : 0.797 14.288 10463 Z= 0.381 Chirality : 0.046 0.188 1183 Planarity : 0.005 0.078 1327 Dihedral : 6.516 47.744 1045 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.12 % Allowed : 28.49 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.27), residues: 946 helix: -0.29 (0.26), residues: 405 sheet: -2.52 (0.58), residues: 72 loop : -2.53 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 548 TYR 0.025 0.002 TYR A 633 PHE 0.023 0.001 PHE A 811 TRP 0.032 0.002 TRP A 957 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7739) covalent geometry : angle 0.79723 (10463) hydrogen bonds : bond 0.03056 ( 265) hydrogen bonds : angle 5.13607 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.7800 (tp40) cc_final: 0.7543 (tt0) REVERT: A 521 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7284 (ptt) REVERT: A 568 LYS cc_start: 0.8064 (tptp) cc_final: 0.7817 (tptp) REVERT: A 688 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7245 (pp20) REVERT: A 701 MET cc_start: 0.5686 (mmt) cc_final: 0.5274 (mmm) REVERT: A 756 MET cc_start: 0.6964 (ptp) cc_final: 0.6676 (ptp) REVERT: A 831 TRP cc_start: 0.7327 (OUTLIER) cc_final: 0.7005 (t-100) REVERT: A 915 LEU cc_start: 0.8701 (tp) cc_final: 0.8429 (tt) REVERT: B 141 TYR cc_start: 0.8717 (m-80) cc_final: 0.8193 (m-80) REVERT: B 162 ILE cc_start: 0.7077 (mp) cc_final: 0.6443 (mp) REVERT: B 163 LYS cc_start: 0.7523 (mmtm) cc_final: 0.7204 (mmtt) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.0848 time to fit residues: 18.3919 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.105557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.085956 restraints weight = 44485.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.089033 restraints weight = 23185.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.090990 restraints weight = 15087.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.092252 restraints weight = 11360.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.093116 restraints weight = 9340.124| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7739 Z= 0.159 Angle : 0.846 14.390 10463 Z= 0.403 Chirality : 0.048 0.293 1183 Planarity : 0.005 0.080 1327 Dihedral : 6.599 46.342 1043 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 4.09 % Allowed : 27.88 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.27), residues: 946 helix: -0.37 (0.26), residues: 399 sheet: -2.70 (0.54), residues: 86 loop : -2.51 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 548 TYR 0.027 0.002 TYR A 633 PHE 0.028 0.002 PHE A 811 TRP 0.038 0.002 TRP A 241 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7739) covalent geometry : angle 0.84566 (10463) hydrogen bonds : bond 0.03328 ( 265) hydrogen bonds : angle 5.28749 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7263 (ptt) REVERT: A 688 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7232 (pp20) REVERT: A 701 MET cc_start: 0.5832 (mmt) cc_final: 0.5423 (mmm) REVERT: A 756 MET cc_start: 0.7052 (ptp) cc_final: 0.6756 (ptp) REVERT: A 872 ILE cc_start: 0.8964 (mp) cc_final: 0.8602 (tp) REVERT: A 915 LEU cc_start: 0.8635 (tp) cc_final: 0.8350 (tt) REVERT: B 141 TYR cc_start: 0.8730 (m-80) cc_final: 0.8179 (m-80) REVERT: B 162 ILE cc_start: 0.7225 (mp) cc_final: 0.6511 (mp) REVERT: B 163 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7365 (mmtt) outliers start: 34 outliers final: 27 residues processed: 153 average time/residue: 0.0861 time to fit residues: 18.2530 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 822 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 65 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 28 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 overall best weight: 0.1572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.109537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.088130 restraints weight = 60485.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.091943 restraints weight = 27935.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094376 restraints weight = 16943.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.095991 restraints weight = 12114.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.097061 restraints weight = 9598.504| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7739 Z= 0.125 Angle : 0.861 15.996 10463 Z= 0.398 Chirality : 0.048 0.368 1183 Planarity : 0.005 0.079 1327 Dihedral : 6.372 48.540 1043 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.52 % Allowed : 28.85 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.27), residues: 946 helix: -0.39 (0.26), residues: 408 sheet: -2.43 (0.54), residues: 83 loop : -2.48 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 548 TYR 0.025 0.002 TYR A 633 PHE 0.034 0.002 PHE B 142 TRP 0.039 0.003 TRP A 241 HIS 0.011 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7739) covalent geometry : angle 0.86109 (10463) hydrogen bonds : bond 0.03088 ( 265) hydrogen bonds : angle 5.21974 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.8014 (m90) cc_final: 0.6933 (t-90) REVERT: A 521 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7200 (ptt) REVERT: A 548 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8123 (tpt90) REVERT: A 688 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7097 (pp20) REVERT: A 701 MET cc_start: 0.5529 (mmt) cc_final: 0.5127 (mmm) REVERT: A 756 MET cc_start: 0.7015 (ptp) cc_final: 0.6776 (ptp) REVERT: A 872 ILE cc_start: 0.8847 (mp) cc_final: 0.8468 (tp) REVERT: B 141 TYR cc_start: 0.8716 (m-80) cc_final: 0.8185 (m-80) REVERT: B 162 ILE cc_start: 0.6978 (mp) cc_final: 0.6476 (mp) REVERT: B 163 LYS cc_start: 0.7470 (mmtm) cc_final: 0.7160 (mmtt) outliers start: 21 outliers final: 15 residues processed: 157 average time/residue: 0.0862 time to fit residues: 18.4643 Evaluate side-chains 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 629 PHE Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 782 HIS Chi-restraints excluded: chain A residue 831 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.0570 chunk 52 optimal weight: 0.0070 chunk 12 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.3328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS A 422 GLN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.109979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.088688 restraints weight = 60684.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.092485 restraints weight = 27772.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.094942 restraints weight = 16941.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.096498 restraints weight = 12125.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.097594 restraints weight = 9613.381| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7739 Z= 0.125 Angle : 0.868 16.205 10463 Z= 0.400 Chirality : 0.048 0.360 1183 Planarity : 0.005 0.078 1327 Dihedral : 6.127 47.203 1043 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.28 % Allowed : 30.41 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.27), residues: 946 helix: -0.47 (0.25), residues: 408 sheet: -2.44 (0.53), residues: 84 loop : -2.45 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.027 0.002 TYR A 633 PHE 0.026 0.001 PHE B 142 TRP 0.050 0.003 TRP A 241 HIS 0.007 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7739) covalent geometry : angle 0.86817 (10463) hydrogen bonds : bond 0.03095 ( 265) hydrogen bonds : angle 5.21752 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1982.74 seconds wall clock time: 34 minutes 51.44 seconds (2091.44 seconds total)