Starting phenix.real_space_refine on Tue Sep 24 09:15:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_0476.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_0476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_0476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_0476.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/09_2024/6npy_0476.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} 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: 5.21, per 1000 atoms: 0.69 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.87 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: 2.12 Time building geometry restraints manager: 2.14 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: 0.960 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.010 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.500 ------------------------------------------------------------------------------- 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= 0.407 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP A 241 HIS 0.011 0.002 HIS A 698 PHE 0.045 0.003 PHE A 648 TYR 0.029 0.003 TYR A 531 ARG 0.005 0.001 ARG B 121 *********************** 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 fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.939 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: 0.2573 time to fit residues: 55.9172 Evaluate side-chains 132 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 80 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7739 Z= 0.248 Angle : 0.834 10.081 10463 Z= 0.417 Chirality : 0.046 0.252 1183 Planarity : 0.006 0.078 1327 Dihedral : 8.224 56.193 1048 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 3.73 % Allowed : 20.19 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.24), residues: 946 helix: -1.65 (0.22), residues: 419 sheet: -3.53 (0.50), residues: 79 loop : -3.09 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 957 HIS 0.005 0.001 HIS A 312 PHE 0.020 0.002 PHE A 648 TYR 0.021 0.002 TYR A 570 ARG 0.008 0.001 ARG B 121 *********************** 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 171 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7766 (m90) cc_final: 0.7517 (m90) REVERT: A 571 LEU cc_start: 0.7559 (mt) cc_final: 0.6865 (mt) REVERT: A 620 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 630 TYR cc_start: 0.8251 (m-80) cc_final: 0.8044 (m-80) REVERT: A 701 MET cc_start: 0.5685 (mmt) cc_final: 0.5413 (mmm) REVERT: A 782 HIS cc_start: 0.6832 (t-90) cc_final: 0.6540 (t70) REVERT: A 816 LEU cc_start: 0.8687 (mt) cc_final: 0.8478 (tp) REVERT: B 162 ILE cc_start: 0.7206 (mp) cc_final: 0.6634 (mp) REVERT: B 163 LYS cc_start: 0.7502 (mmtm) cc_final: 0.7301 (mmtt) REVERT: B 207 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6929 (mmm160) REVERT: B 241 MET cc_start: 0.6004 (ppp) cc_final: 0.5452 (ppp) outliers start: 31 outliers final: 23 residues processed: 162 average time/residue: 0.2105 time to fit residues: 45.1185 Evaluate side-chains 147 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.192 Angle : 0.773 8.925 10463 Z= 0.381 Chirality : 0.045 0.258 1183 Planarity : 0.005 0.073 1327 Dihedral : 7.727 59.369 1048 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.93 % Allowed : 21.03 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.26), residues: 946 helix: -1.05 (0.24), residues: 413 sheet: -3.25 (0.50), residues: 79 loop : -2.84 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 957 HIS 0.003 0.001 HIS B 125 PHE 0.027 0.002 PHE A 811 TYR 0.016 0.002 TYR A 570 ARG 0.007 0.001 ARG B 121 *********************** 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 182 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7717 (m90) cc_final: 0.7474 (m90) REVERT: A 521 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6448 (ptt) REVERT: A 571 LEU cc_start: 0.7411 (mt) cc_final: 0.6677 (mt) REVERT: A 630 TYR cc_start: 0.8276 (m-80) cc_final: 0.8065 (m-80) REVERT: A 701 MET cc_start: 0.5572 (mmt) cc_final: 0.5298 (mmm) REVERT: A 782 HIS cc_start: 0.6714 (t-90) cc_final: 0.6419 (t-90) REVERT: B 162 ILE cc_start: 0.7051 (mp) cc_final: 0.6394 (mp) REVERT: B 163 LYS cc_start: 0.7430 (mmtm) cc_final: 0.7224 (mmtt) REVERT: B 213 TYR cc_start: 0.4063 (t80) cc_final: 0.3812 (t80) REVERT: B 265 GLU cc_start: 0.7063 (tp30) cc_final: 0.6838 (tt0) outliers start: 41 outliers final: 23 residues processed: 169 average time/residue: 0.2014 time to fit residues: 45.4944 Evaluate side-chains 150 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 719 VAL Chi-restraints excluded: chain A residue 787 ASP 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 844 ASP Chi-restraints excluded: chain A residue 895 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7739 Z= 0.282 Angle : 0.837 10.818 10463 Z= 0.414 Chirality : 0.049 0.248 1183 Planarity : 0.005 0.085 1327 Dihedral : 7.621 58.033 1045 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 4.93 % Allowed : 22.36 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.26), residues: 946 helix: -0.87 (0.25), residues: 412 sheet: -3.37 (0.49), residues: 79 loop : -2.72 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 241 HIS 0.005 0.001 HIS A 312 PHE 0.023 0.002 PHE A 648 TYR 0.015 0.002 TYR A 256 ARG 0.007 0.001 ARG A 548 *********************** 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 168 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6593 (ptt) REVERT: A 701 MET cc_start: 0.5825 (mmt) cc_final: 0.5518 (mmm) REVERT: B 162 ILE cc_start: 0.7261 (mp) cc_final: 0.6624 (mp) REVERT: B 163 LYS cc_start: 0.7761 (mmtm) cc_final: 0.7478 (mmtt) REVERT: B 213 TYR cc_start: 0.4136 (t80) cc_final: 0.3838 (t80) outliers start: 41 outliers final: 32 residues processed: 156 average time/residue: 0.1943 time to fit residues: 41.0289 Evaluate side-chains 153 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 280 ASP Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 532 TYR 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 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 842 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 795 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.184 Angle : 0.766 10.585 10463 Z= 0.373 Chirality : 0.046 0.224 1183 Planarity : 0.005 0.079 1327 Dihedral : 7.167 54.540 1045 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.97 % Allowed : 23.92 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 946 helix: -0.53 (0.26), residues: 405 sheet: -3.15 (0.50), residues: 81 loop : -2.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 957 HIS 0.006 0.001 HIS A 782 PHE 0.018 0.001 PHE B 142 TYR 0.012 0.001 TYR A1007 ARG 0.007 0.001 ARG A 488 *********************** 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 173 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7768 (m90) cc_final: 0.7445 (m90) REVERT: A 521 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6531 (ptt) REVERT: A 637 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7033 (tt0) REVERT: A 641 VAL cc_start: 0.8536 (t) cc_final: 0.7775 (t) REVERT: A 701 MET cc_start: 0.5631 (mmt) cc_final: 0.5323 (mmm) REVERT: A 915 LEU cc_start: 0.8719 (tp) cc_final: 0.8412 (tt) REVERT: B 162 ILE cc_start: 0.7075 (mp) cc_final: 0.6449 (mp) REVERT: B 163 LYS cc_start: 0.7533 (mmtm) cc_final: 0.7239 (mmtt) REVERT: B 213 TYR cc_start: 0.4012 (t80) cc_final: 0.3710 (t80) outliers start: 33 outliers final: 26 residues processed: 163 average time/residue: 0.2049 time to fit residues: 46.3935 Evaluate side-chains 157 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 254 LEU 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 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 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 804 SER 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 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 30 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 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 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3193 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= 0.187 Angle : 0.790 11.701 10463 Z= 0.379 Chirality : 0.047 0.303 1183 Planarity : 0.005 0.081 1327 Dihedral : 6.902 48.747 1045 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 4.09 % Allowed : 25.84 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.27), residues: 946 helix: -0.45 (0.26), residues: 406 sheet: -3.03 (0.51), residues: 81 loop : -2.52 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 957 HIS 0.003 0.001 HIS A 782 PHE 0.016 0.001 PHE A 302 TYR 0.021 0.001 TYR A 630 ARG 0.006 0.000 ARG A 488 *********************** 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 169 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7703 (m90) cc_final: 0.6912 (t-170) REVERT: A 521 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6475 (ptt) REVERT: A 637 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6818 (tt0) REVERT: A 641 VAL cc_start: 0.8480 (t) cc_final: 0.7595 (t) REVERT: A 688 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: A 701 MET cc_start: 0.5597 (mmt) cc_final: 0.5247 (mmm) REVERT: A 790 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 915 LEU cc_start: 0.8795 (tp) cc_final: 0.8561 (tt) REVERT: B 162 ILE cc_start: 0.7002 (mp) cc_final: 0.6386 (mp) REVERT: B 163 LYS cc_start: 0.7484 (mmtm) cc_final: 0.7187 (mmtt) REVERT: B 213 TYR cc_start: 0.3952 (t80) cc_final: 0.3691 (t80) outliers start: 34 outliers final: 23 residues processed: 161 average time/residue: 0.1799 time to fit residues: 40.1212 Evaluate side-chains 152 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 787 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 SER 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 225 LEU 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 10 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 91 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3494 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= 0.177 Angle : 0.776 14.349 10463 Z= 0.372 Chirality : 0.046 0.179 1183 Planarity : 0.005 0.080 1327 Dihedral : 6.610 48.807 1045 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.37 % Allowed : 27.16 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.27), residues: 946 helix: -0.38 (0.26), residues: 406 sheet: -2.53 (0.58), residues: 72 loop : -2.55 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 957 HIS 0.004 0.001 HIS A 782 PHE 0.024 0.001 PHE B 142 TYR 0.049 0.002 TYR A 630 ARG 0.009 0.001 ARG A 548 *********************** 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 167 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7712 (m90) cc_final: 0.6921 (t-170) REVERT: A 521 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6497 (ptt) REVERT: A 641 VAL cc_start: 0.8429 (t) cc_final: 0.7961 (t) REVERT: A 688 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: A 701 MET cc_start: 0.5493 (mmt) cc_final: 0.5132 (mmm) REVERT: A 756 MET cc_start: 0.7014 (ptp) cc_final: 0.6728 (ptp) REVERT: A 790 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8971 (mm) REVERT: B 162 ILE cc_start: 0.6925 (mp) cc_final: 0.6339 (mp) REVERT: B 163 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7157 (mmtt) REVERT: B 213 TYR cc_start: 0.3849 (t80) cc_final: 0.3608 (t80) outliers start: 28 outliers final: 24 residues processed: 161 average time/residue: 0.1873 time to fit residues: 40.9455 Evaluate side-chains 154 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 790 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 804 SER 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 225 LEU 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 54 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 58 optimal weight: 0.0270 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 1.3840 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.3613 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= 0.195 Angle : 0.787 11.100 10463 Z= 0.382 Chirality : 0.046 0.173 1183 Planarity : 0.005 0.075 1327 Dihedral : 6.497 47.115 1044 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 3.12 % Allowed : 28.12 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.27), residues: 946 helix: -0.32 (0.26), residues: 405 sheet: -2.59 (0.58), residues: 72 loop : -2.52 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 957 HIS 0.005 0.001 HIS A 782 PHE 0.018 0.001 PHE A 302 TYR 0.045 0.002 TYR A 630 ARG 0.007 0.000 ARG A 918 *********************** 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 158 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 HIS cc_start: 0.7737 (m90) cc_final: 0.6898 (t-170) REVERT: A 521 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6536 (ptt) REVERT: A 688 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: A 701 MET cc_start: 0.5558 (mmt) cc_final: 0.5201 (mmm) REVERT: A 756 MET cc_start: 0.7136 (ptp) cc_final: 0.6788 (ptp) REVERT: A 790 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9004 (mm) REVERT: A 831 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.7149 (t-100) REVERT: A 872 ILE cc_start: 0.8863 (mp) cc_final: 0.8534 (tp) REVERT: B 162 ILE cc_start: 0.6930 (mp) cc_final: 0.6434 (mp) REVERT: B 163 LYS cc_start: 0.7462 (mmtm) cc_final: 0.7160 (mmtt) REVERT: B 218 ASP cc_start: 0.8347 (m-30) cc_final: 0.8136 (m-30) outliers start: 26 outliers final: 20 residues processed: 152 average time/residue: 0.1927 time to fit residues: 39.8985 Evaluate side-chains 152 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 GLU 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 787 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 795 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3832 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= 0.182 Angle : 0.785 11.316 10463 Z= 0.377 Chirality : 0.046 0.168 1183 Planarity : 0.005 0.073 1327 Dihedral : 6.354 48.472 1043 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 3.25 % Allowed : 28.85 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.27), residues: 946 helix: -0.39 (0.26), residues: 404 sheet: -2.50 (0.56), residues: 77 loop : -2.56 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 241 HIS 0.005 0.001 HIS A 782 PHE 0.022 0.001 PHE A 811 TYR 0.031 0.001 TYR A 633 ARG 0.012 0.001 ARG A 548 *********************** 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 160 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.867 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: 0.7720 (m90) cc_final: 0.6829 (t-170) REVERT: A 521 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6554 (ptt) REVERT: A 688 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: A 701 MET cc_start: 0.5477 (mmt) cc_final: 0.5114 (mmm) REVERT: A 756 MET cc_start: 0.7104 (ptp) cc_final: 0.6813 (ptp) REVERT: A 790 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9020 (mm) REVERT: A 801 LEU cc_start: 0.9035 (tt) cc_final: 0.8796 (tp) REVERT: A 831 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.7099 (t-100) REVERT: A 872 ILE cc_start: 0.8808 (mp) cc_final: 0.8488 (tp) REVERT: B 162 ILE cc_start: 0.6858 (mp) cc_final: 0.6426 (mp) REVERT: B 163 LYS cc_start: 0.7428 (mmtm) cc_final: 0.7136 (mmtt) outliers start: 27 outliers final: 20 residues processed: 154 average time/residue: 0.1808 time to fit residues: 38.2611 Evaluate side-chains 153 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 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 790 LEU Chi-restraints excluded: chain A residue 795 ASN 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 225 LEU 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 42 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7739 Z= 0.188 Angle : 0.798 11.481 10463 Z= 0.382 Chirality : 0.046 0.167 1183 Planarity : 0.005 0.072 1327 Dihedral : 6.276 47.676 1043 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.88 % Allowed : 29.45 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.27), residues: 946 helix: -0.42 (0.25), residues: 406 sheet: -2.46 (0.54), residues: 83 loop : -2.49 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 241 HIS 0.011 0.001 HIS A 218 PHE 0.029 0.001 PHE A 648 TYR 0.044 0.002 TYR A 630 ARG 0.014 0.001 ARG A 548 ********************** 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 153 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6540 (ptt) REVERT: A 688 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7366 (pp20) REVERT: A 701 MET cc_start: 0.5512 (mmt) cc_final: 0.5150 (mmm) REVERT: A 756 MET cc_start: 0.7261 (ptp) cc_final: 0.6961 (ptp) REVERT: A 790 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9031 (mm) REVERT: A 801 LEU cc_start: 0.9043 (tt) cc_final: 0.8819 (tp) REVERT: A 872 ILE cc_start: 0.8803 (mp) cc_final: 0.8483 (tp) REVERT: B 162 ILE cc_start: 0.6813 (mp) cc_final: 0.6275 (mp) REVERT: B 163 LYS cc_start: 0.7419 (mmtm) cc_final: 0.7132 (mmtt) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.1898 time to fit residues: 39.0017 Evaluate side-chains 149 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 688 GLU 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 790 LEU Chi-restraints excluded: chain A residue 795 ASN 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 225 LEU 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 69 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.109082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.088334 restraints weight = 56464.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.092031 restraints weight = 25902.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.094366 restraints weight = 15864.843| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3932 r_free = 0.3932 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4075 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= 0.186 Angle : 0.806 11.795 10463 Z= 0.384 Chirality : 0.046 0.191 1183 Planarity : 0.005 0.071 1327 Dihedral : 6.188 47.752 1043 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.00 % Allowed : 29.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.27), residues: 946 helix: -0.46 (0.26), residues: 405 sheet: -2.35 (0.55), residues: 83 loop : -2.47 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 241 HIS 0.006 0.001 HIS A 822 PHE 0.029 0.001 PHE B 142 TYR 0.049 0.002 TYR A 630 ARG 0.013 0.001 ARG A 548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.14 seconds wall clock time: 35 minutes 53.17 seconds (2153.17 seconds total)