Starting phenix.real_space_refine on Wed Mar 12 09:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.map" model { file = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xou_22280/03_2025/6xou_22280.cif" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4897 2.51 5 N 1304 2.21 5 O 1457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7697 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7697 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 965, 7691 Classifications: {'peptide': 965} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 902} Chain breaks: 1 bond proxies already assigned to first conformer: 7875 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 723 " occ=0.42 ... (10 atoms not shown) pdb=" OG BSER A 723 " occ=0.58 Time building chain proxies: 8.55, per 1000 atoms: 1.11 Number of scatterers: 7697 At special positions: 0 Unit cell: (84.744, 98.44, 103.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1457 8.00 N 1304 7.00 C 4897 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: 1.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1824 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 7 sheets defined 53.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.096A pdb=" N ARG A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.927A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.532A pdb=" N MET A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.725A pdb=" N VAL A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.866A pdb=" N GLU A 244 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.916A pdb=" N HIS A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 400 through 419 Processing helix chain 'A' and resid 421 through 438 removed outlier: 3.566A pdb=" N ILE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 457 removed outlier: 4.750A pdb=" N SER A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N CYS A 454 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 481 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 530 through 550 Processing helix chain 'A' and resid 608 through 613 removed outlier: 3.639A pdb=" N ARG A 612 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Proline residue: A 613 - end of helix Processing helix chain 'A' and resid 614 through 622 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 695 through 713 removed outlier: 3.703A pdb=" N PHE A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.550A pdb=" N VAL A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 763 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.294A pdb=" N ARG A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 802 Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.323A pdb=" N SER A 882 " --> pdb=" O PRO A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 928 through 945 removed outlier: 3.505A pdb=" N LEU A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 964 Processing helix chain 'A' and resid 968 through 972 removed outlier: 3.566A pdb=" N LYS A 972 " --> pdb=" O PRO A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.947A pdb=" N PHE A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 997 through 1008 Processing helix chain 'A' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET A 135 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 149 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.798A pdb=" N LYS A 66 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 54 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 64 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 56 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 62 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A 75 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR A 267 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 77 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 186 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 373 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 313 removed outlier: 5.721A pdb=" N THR A 326 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 387 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 575 through 579 removed outlier: 3.554A pdb=" N ASP A 575 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL A 782 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN A 586 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA A 784 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS A 588 " --> pdb=" O ALA A 784 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 598 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY A 645 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 673 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 643 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 912 removed outlier: 6.325A pdb=" N THR A 855 " --> pdb=" O ILE A1020 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY A1022 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N PHE A 857 " --> pdb=" O GLY A1022 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS A 854 " --> pdb=" O ILE A1035 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.31 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: 2447 1.34 - 1.46: 1495 1.46 - 1.58: 3885 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 7889 Sorted by residual: bond pdb=" C ILE A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.46e+00 bond pdb=" C ILE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.76e+00 bond pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 bond pdb=" CB ASN A 712 " pdb=" CG ASN A 712 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.40e+00 bond pdb=" CG1 ILE A 885 " pdb=" CD1 ILE A 885 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.10e+00 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 10166 2.10 - 4.20: 422 4.20 - 6.30: 66 6.30 - 8.40: 28 8.40 - 10.50: 16 Bond angle restraints: 10698 Sorted by residual: angle pdb=" N ASP A 458 " pdb=" CA ASP A 458 " pdb=" C ASP A 458 " ideal model delta sigma weight residual 111.54 117.53 -5.99 1.36e+00 5.41e-01 1.94e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.30 106.10 5.20 1.43e+00 4.89e-01 1.32e+01 angle pdb=" C ALA A 580 " pdb=" N GLY A 581 " pdb=" CA GLY A 581 " ideal model delta sigma weight residual 121.70 128.18 -6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" C LYS A 893 " pdb=" N PHE A 894 " pdb=" CA PHE A 894 " ideal model delta sigma weight residual 121.54 114.71 6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" CA VAL A 615 " pdb=" C VAL A 615 " pdb=" N PRO A 616 " ideal model delta sigma weight residual 118.88 124.27 -5.39 1.54e+00 4.22e-01 1.23e+01 ... (remaining 10693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4386 17.76 - 35.52: 295 35.52 - 53.27: 65 53.27 - 71.03: 15 71.03 - 88.79: 10 Dihedral angle restraints: 4771 sinusoidal: 1952 harmonic: 2819 Sorted by residual: dihedral pdb=" CA PHE A 210 " pdb=" C PHE A 210 " pdb=" N THR A 211 " pdb=" CA THR A 211 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO A 170 " pdb=" C PRO A 170 " pdb=" N CYS A 171 " pdb=" CA CYS A 171 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C VAL A 102 " pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" CB VAL A 102 " ideal model delta harmonic sigma weight residual -122.00 -131.21 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 921 0.070 - 0.140: 213 0.140 - 0.209: 32 0.209 - 0.279: 5 0.279 - 0.349: 1 Chirality restraints: 1172 Sorted by residual: chirality pdb=" CG LEU A 467 " pdb=" CB LEU A 467 " pdb=" CD1 LEU A 467 " pdb=" CD2 LEU A 467 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR A 94 " pdb=" CA THR A 94 " pdb=" OG1 THR A 94 " pdb=" CG2 THR A 94 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1169 not shown) Planarity restraints: 1397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 301 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR A 301 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 301 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 302 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 334 " -0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 335 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 793 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C GLU A 793 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU A 793 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 794 " -0.012 2.00e-02 2.50e+03 ... (remaining 1394 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1748 2.79 - 3.32: 6901 3.32 - 3.84: 12652 3.84 - 4.37: 14147 4.37 - 4.90: 24954 Nonbonded interactions: 60402 Sorted by model distance: nonbonded pdb=" ND2 ASN A 783 " pdb=" O PRO A 969 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR A 146 " pdb=" OH TYR A 258 " model vdw 2.270 3.040 nonbonded pdb=" O SER A 351 " pdb=" OG SER A 355 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP A 98 " pdb=" OG1 THR A 100 " model vdw 2.302 3.040 nonbonded pdb=" O HIS A 457 " pdb=" OD1 ASP A 458 " model vdw 2.310 3.040 ... (remaining 60397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.005 0.075 7889 Z= 0.332 Angle : 1.064 10.498 10698 Z= 0.563 Chirality : 0.061 0.349 1172 Planarity : 0.007 0.056 1397 Dihedral : 13.628 88.791 2947 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.23 % Allowed : 2.10 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.51 (0.24), residues: 964 helix: -1.05 (0.21), residues: 447 sheet: 0.29 (0.36), residues: 178 loop : -1.42 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 684 HIS 0.008 0.001 HIS A 430 PHE 0.021 0.002 PHE A 848 TYR 0.016 0.002 TYR A 662 ARG 0.006 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.8860 (m) cc_final: 0.8624 (p) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2273 time to fit residues: 47.1088 Evaluate side-chains 94 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 151 GLN A 204 ASN A 325 GLN A 430 HIS A 637 GLN A 638 GLN A 690 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.043842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.034548 restraints weight = 46633.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035932 restraints weight = 27161.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.036926 restraints weight = 18348.458| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7889 Z= 0.297 Angle : 0.789 10.700 10698 Z= 0.397 Chirality : 0.045 0.194 1172 Planarity : 0.005 0.044 1397 Dihedral : 4.440 22.702 1036 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.52 % Allowed : 11.79 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 964 helix: 0.75 (0.24), residues: 453 sheet: 1.01 (0.38), residues: 179 loop : -0.86 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 455 HIS 0.005 0.001 HIS A 108 PHE 0.023 0.002 PHE A 918 TYR 0.013 0.002 TYR A 268 ARG 0.003 0.001 ARG A 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9569 (tp) cc_final: 0.9365 (tp) REVERT: A 388 TYR cc_start: 0.9336 (p90) cc_final: 0.8840 (p90) REVERT: A 400 ASP cc_start: 0.9090 (t0) cc_final: 0.8784 (t0) REVERT: A 595 MET cc_start: 0.8296 (mmm) cc_final: 0.8093 (mmm) REVERT: A 918 PHE cc_start: 0.9351 (t80) cc_final: 0.9146 (t80) outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1740 time to fit residues: 24.6726 Evaluate side-chains 84 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 851 TRP Chi-restraints excluded: chain A residue 866 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.044824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.035457 restraints weight = 46878.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036911 restraints weight = 26702.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.037940 restraints weight = 17942.734| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7889 Z= 0.197 Angle : 0.727 11.969 10698 Z= 0.357 Chirality : 0.043 0.162 1172 Planarity : 0.005 0.045 1397 Dihedral : 4.246 19.784 1036 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.58 % Allowed : 12.49 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 964 helix: 1.07 (0.24), residues: 460 sheet: 1.24 (0.38), residues: 170 loop : -0.67 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 455 HIS 0.003 0.001 HIS A 108 PHE 0.020 0.001 PHE A 918 TYR 0.011 0.001 TYR A 268 ARG 0.003 0.000 ARG A 924 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9530 (tp) cc_final: 0.9317 (tp) REVERT: A 123 PHE cc_start: 0.8273 (t80) cc_final: 0.7399 (t80) REVERT: A 126 MET cc_start: 0.8882 (tpt) cc_final: 0.8640 (tpt) REVERT: A 225 LEU cc_start: 0.9542 (mt) cc_final: 0.9284 (mt) REVERT: A 388 TYR cc_start: 0.9284 (p90) cc_final: 0.8858 (p90) REVERT: A 400 ASP cc_start: 0.8982 (t0) cc_final: 0.8529 (t0) REVERT: A 527 GLU cc_start: 0.9209 (pp20) cc_final: 0.8997 (pp20) REVERT: A 595 MET cc_start: 0.8364 (mmm) cc_final: 0.8125 (mmm) REVERT: A 853 MET cc_start: 0.8372 (mmt) cc_final: 0.8154 (mmp) REVERT: A 911 LYS cc_start: 0.9059 (mttt) cc_final: 0.8810 (mtmm) REVERT: A 974 MET cc_start: 0.8637 (tpp) cc_final: 0.8362 (tpp) outliers start: 3 outliers final: 2 residues processed: 89 average time/residue: 0.1714 time to fit residues: 22.4541 Evaluate side-chains 79 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 851 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- 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 = 0.2998 r_free = 0.2998 target = 0.044118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034978 restraints weight = 47291.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.036388 restraints weight = 26823.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.037399 restraints weight = 17916.078| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.212 Angle : 0.718 13.791 10698 Z= 0.347 Chirality : 0.043 0.147 1172 Planarity : 0.004 0.042 1397 Dihedral : 4.136 19.862 1036 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.70 % Allowed : 14.00 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 964 helix: 1.25 (0.24), residues: 466 sheet: 1.19 (0.37), residues: 170 loop : -0.45 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 455 HIS 0.003 0.001 HIS A 108 PHE 0.013 0.001 PHE A 474 TYR 0.011 0.001 TYR A 632 ARG 0.003 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9539 (tp) cc_final: 0.9150 (tp) REVERT: A 225 LEU cc_start: 0.9537 (mt) cc_final: 0.9311 (mt) REVERT: A 388 TYR cc_start: 0.9243 (p90) cc_final: 0.8843 (p90) REVERT: A 400 ASP cc_start: 0.9049 (t0) cc_final: 0.8595 (t0) REVERT: A 455 TRP cc_start: 0.9009 (t60) cc_final: 0.8736 (t60) REVERT: A 527 GLU cc_start: 0.9215 (pp20) cc_final: 0.9010 (pp20) REVERT: A 582 ASP cc_start: 0.9435 (p0) cc_final: 0.9152 (t0) REVERT: A 595 MET cc_start: 0.8360 (mmm) cc_final: 0.7963 (mmm) REVERT: A 681 MET cc_start: 0.9457 (mmm) cc_final: 0.9106 (mmp) REVERT: A 755 MET cc_start: 0.8770 (mpp) cc_final: 0.8526 (mpp) REVERT: A 1030 LYS cc_start: 0.9247 (ptpp) cc_final: 0.9032 (ptpp) outliers start: 4 outliers final: 4 residues processed: 78 average time/residue: 0.1713 time to fit residues: 19.5537 Evaluate side-chains 76 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 851 TRP Chi-restraints excluded: chain A residue 866 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3023 r_free = 0.3023 target = 0.044772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035485 restraints weight = 47283.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.036921 restraints weight = 26830.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.037941 restraints weight = 17877.967| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.182 Angle : 0.710 12.226 10698 Z= 0.338 Chirality : 0.042 0.143 1172 Planarity : 0.004 0.043 1397 Dihedral : 4.105 20.732 1036 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.17 % Allowed : 13.89 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.07 (0.27), residues: 964 helix: 1.32 (0.24), residues: 464 sheet: 1.15 (0.37), residues: 170 loop : -0.31 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 455 HIS 0.003 0.001 HIS A 229 PHE 0.021 0.001 PHE A 598 TYR 0.010 0.001 TYR A 923 ARG 0.002 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9526 (tp) cc_final: 0.9053 (tp) REVERT: A 225 LEU cc_start: 0.9519 (mt) cc_final: 0.9297 (mt) REVERT: A 388 TYR cc_start: 0.9217 (p90) cc_final: 0.8820 (p90) REVERT: A 400 ASP cc_start: 0.9019 (t0) cc_final: 0.8787 (t0) REVERT: A 455 TRP cc_start: 0.9011 (t60) cc_final: 0.8789 (t60) REVERT: A 527 GLU cc_start: 0.9210 (pp20) cc_final: 0.8994 (pp20) REVERT: A 582 ASP cc_start: 0.9387 (p0) cc_final: 0.9146 (t0) REVERT: A 595 MET cc_start: 0.8356 (mmm) cc_final: 0.7951 (mmm) REVERT: A 681 MET cc_start: 0.9375 (mmm) cc_final: 0.8969 (mmp) REVERT: A 911 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8764 (mptt) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.2000 time to fit residues: 24.8275 Evaluate side-chains 75 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 851 TRP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 911 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 275 GLN A 856 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.041765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.032854 restraints weight = 50659.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034208 restraints weight = 28689.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035166 restraints weight = 19197.128| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7889 Z= 0.377 Angle : 0.800 10.166 10698 Z= 0.396 Chirality : 0.045 0.181 1172 Planarity : 0.005 0.038 1397 Dihedral : 4.415 17.918 1036 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 15.05 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 964 helix: 1.21 (0.24), residues: 452 sheet: 0.85 (0.36), residues: 174 loop : -0.43 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 941 HIS 0.007 0.002 HIS A 880 PHE 0.027 0.002 PHE A 123 TYR 0.014 0.002 TYR A 632 ARG 0.003 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9689 (tp) cc_final: 0.9403 (tp) REVERT: A 87 LEU cc_start: 0.8799 (tt) cc_final: 0.8520 (tt) REVERT: A 142 ASP cc_start: 0.8884 (t0) cc_final: 0.8594 (t0) REVERT: A 388 TYR cc_start: 0.9253 (p90) cc_final: 0.8862 (p90) REVERT: A 586 GLN cc_start: 0.9325 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 595 MET cc_start: 0.8282 (mmm) cc_final: 0.7845 (mmm) REVERT: A 681 MET cc_start: 0.9443 (mmm) cc_final: 0.9136 (mmm) outliers start: 13 outliers final: 9 residues processed: 75 average time/residue: 0.2443 time to fit residues: 27.4951 Evaluate side-chains 76 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 918 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1016 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.034438 restraints weight = 48400.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.035871 restraints weight = 27135.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036887 restraints weight = 18003.224| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.189 Angle : 0.765 10.603 10698 Z= 0.360 Chirality : 0.043 0.178 1172 Planarity : 0.004 0.043 1397 Dihedral : 4.146 17.684 1036 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.93 % Allowed : 15.99 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.08 (0.27), residues: 964 helix: 1.40 (0.24), residues: 459 sheet: 0.72 (0.36), residues: 177 loop : -0.14 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 851 HIS 0.003 0.001 HIS A 457 PHE 0.030 0.001 PHE A 123 TYR 0.013 0.001 TYR A 510 ARG 0.004 0.000 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9547 (tp) cc_final: 0.9238 (tp) REVERT: A 87 LEU cc_start: 0.8820 (tt) cc_final: 0.8558 (tt) REVERT: A 388 TYR cc_start: 0.9228 (p90) cc_final: 0.8750 (p90) REVERT: A 400 ASP cc_start: 0.8997 (t0) cc_final: 0.8739 (t0) REVERT: A 582 ASP cc_start: 0.9426 (p0) cc_final: 0.9124 (t0) REVERT: A 586 GLN cc_start: 0.9308 (tt0) cc_final: 0.8715 (tm-30) REVERT: A 595 MET cc_start: 0.8185 (mmm) cc_final: 0.7771 (mmm) REVERT: A 681 MET cc_start: 0.9365 (mmm) cc_final: 0.8944 (mmp) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.1683 time to fit residues: 20.1351 Evaluate side-chains 75 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 92 optimal weight: 0.0270 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.0670 chunk 87 optimal weight: 4.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3008 r_free = 0.3008 target = 0.044204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035050 restraints weight = 48291.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.036505 restraints weight = 27091.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.037530 restraints weight = 17905.753| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7889 Z= 0.181 Angle : 0.770 12.189 10698 Z= 0.359 Chirality : 0.044 0.189 1172 Planarity : 0.004 0.042 1397 Dihedral : 4.048 18.502 1036 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.82 % Allowed : 16.92 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.09 (0.27), residues: 964 helix: 1.35 (0.25), residues: 464 sheet: 0.66 (0.36), residues: 176 loop : 0.00 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 851 HIS 0.004 0.001 HIS A 457 PHE 0.027 0.001 PHE A 123 TYR 0.011 0.001 TYR A 510 ARG 0.002 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9494 (tp) cc_final: 0.9273 (tp) REVERT: A 87 LEU cc_start: 0.8820 (tt) cc_final: 0.8556 (tt) REVERT: A 388 TYR cc_start: 0.9180 (p90) cc_final: 0.8869 (p90) REVERT: A 400 ASP cc_start: 0.9023 (t0) cc_final: 0.8759 (t0) REVERT: A 582 ASP cc_start: 0.9472 (p0) cc_final: 0.9156 (t0) REVERT: A 586 GLN cc_start: 0.9288 (tt0) cc_final: 0.8709 (tm-30) REVERT: A 595 MET cc_start: 0.8213 (mmm) cc_final: 0.7809 (mmm) REVERT: A 681 MET cc_start: 0.9361 (mmm) cc_final: 0.8945 (mmp) REVERT: A 911 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8985 (mptt) outliers start: 5 outliers final: 5 residues processed: 75 average time/residue: 0.1893 time to fit residues: 21.0607 Evaluate side-chains 75 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.043545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034370 restraints weight = 49921.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.035832 restraints weight = 27967.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.036842 restraints weight = 18525.574| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.201 Angle : 0.772 12.851 10698 Z= 0.360 Chirality : 0.044 0.267 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.048 17.701 1036 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.17 % Allowed : 15.87 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.13 (0.27), residues: 964 helix: 1.52 (0.25), residues: 452 sheet: 0.58 (0.36), residues: 176 loop : -0.10 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 851 HIS 0.003 0.001 HIS A 69 PHE 0.026 0.001 PHE A 123 TYR 0.011 0.001 TYR A 510 ARG 0.003 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9524 (tp) cc_final: 0.9301 (tp) REVERT: A 87 LEU cc_start: 0.8817 (tt) cc_final: 0.8478 (tt) REVERT: A 318 PHE cc_start: 0.9373 (m-80) cc_final: 0.9111 (m-80) REVERT: A 388 TYR cc_start: 0.9219 (p90) cc_final: 0.8837 (p90) REVERT: A 400 ASP cc_start: 0.9080 (t0) cc_final: 0.8826 (t0) REVERT: A 582 ASP cc_start: 0.9503 (p0) cc_final: 0.9192 (t0) REVERT: A 586 GLN cc_start: 0.9289 (tt0) cc_final: 0.8683 (tm-30) REVERT: A 595 MET cc_start: 0.8243 (mmm) cc_final: 0.7830 (mmm) REVERT: A 681 MET cc_start: 0.9365 (mmm) cc_final: 0.8937 (mmp) REVERT: A 743 MET cc_start: 0.9107 (mmm) cc_final: 0.8871 (mmp) REVERT: A 911 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8888 (mptt) REVERT: A 975 ASP cc_start: 0.9098 (p0) cc_final: 0.8728 (t0) REVERT: A 1006 ASP cc_start: 0.8878 (t70) cc_final: 0.8465 (p0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1796 time to fit residues: 22.0692 Evaluate side-chains 77 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 71 optimal weight: 0.4980 chunk 16 optimal weight: 0.2980 chunk 77 optimal weight: 0.0050 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 = 0.2988 r_free = 0.2988 target = 0.043615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034507 restraints weight = 48500.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.035936 restraints weight = 27480.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.036952 restraints weight = 18348.124| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7889 Z= 0.200 Angle : 0.784 11.942 10698 Z= 0.364 Chirality : 0.044 0.320 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.058 18.372 1036 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.05 % Allowed : 16.34 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.13 (0.27), residues: 964 helix: 1.46 (0.25), residues: 459 sheet: 0.51 (0.36), residues: 176 loop : 0.02 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 851 HIS 0.003 0.001 HIS A 457 PHE 0.026 0.001 PHE A 123 TYR 0.011 0.001 TYR A 510 ARG 0.003 0.000 ARG A 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9533 (tp) cc_final: 0.9311 (tp) REVERT: A 87 LEU cc_start: 0.8828 (tt) cc_final: 0.8478 (tt) REVERT: A 318 PHE cc_start: 0.9366 (m-80) cc_final: 0.9105 (m-80) REVERT: A 388 TYR cc_start: 0.9221 (p90) cc_final: 0.8806 (p90) REVERT: A 400 ASP cc_start: 0.9051 (t0) cc_final: 0.8794 (t0) REVERT: A 582 ASP cc_start: 0.9498 (p0) cc_final: 0.9194 (t0) REVERT: A 586 GLN cc_start: 0.9287 (tt0) cc_final: 0.8663 (tm-30) REVERT: A 595 MET cc_start: 0.8204 (mmm) cc_final: 0.7834 (mmm) REVERT: A 681 MET cc_start: 0.9375 (mmm) cc_final: 0.8983 (mmp) REVERT: A 911 LYS cc_start: 0.9186 (ptpp) cc_final: 0.8907 (mptt) REVERT: A 975 ASP cc_start: 0.9112 (p0) cc_final: 0.8745 (t0) REVERT: A 1006 ASP cc_start: 0.8886 (t70) cc_final: 0.8490 (p0) outliers start: 7 outliers final: 7 residues processed: 75 average time/residue: 0.2165 time to fit residues: 25.9582 Evaluate side-chains 76 residues out of total 855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3005 r_free = 0.3005 target = 0.044104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.034895 restraints weight = 48840.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036356 restraints weight = 27597.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037392 restraints weight = 18333.033| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7889 Z= 0.184 Angle : 0.779 12.572 10698 Z= 0.358 Chirality : 0.044 0.322 1172 Planarity : 0.004 0.041 1397 Dihedral : 4.008 18.897 1036 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.05 % Allowed : 16.45 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.15 (0.27), residues: 964 helix: 1.46 (0.25), residues: 459 sheet: 0.51 (0.36), residues: 176 loop : 0.07 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 851 HIS 0.003 0.001 HIS A 457 PHE 0.026 0.001 PHE A 123 TYR 0.011 0.001 TYR A 510 ARG 0.003 0.000 ARG A 599 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3236.36 seconds wall clock time: 59 minutes 11.26 seconds (3551.26 seconds total)