Starting phenix.real_space_refine on Wed Feb 12 00:54:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwu_35780/02_2025/8iwu_35780.cif" } resolution = 3.31 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= 0.019 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 52 5.16 5 C 4358 2.51 5 N 1142 2.21 5 O 1285 1.98 5 F 4 1.80 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-5592/modules/chem_data/mon_lib" Total number of atoms: 6843 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6837 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 35, 'TRANS': 857} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.61, per 1000 atoms: 0.67 Number of scatterers: 6843 At special positions: 0 Unit cell: (89.88, 91.56, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 52 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1285 8.00 N 1142 7.00 C 4358 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 55.9% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 99 through 121 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.785A pdb=" N LEU A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 256 through 288 Processing helix chain 'A' and resid 290 through 306 removed outlier: 3.904A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.393A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.674A pdb=" N VAL A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.973A pdb=" N LYS A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 551 through 563 removed outlier: 4.060A pdb=" N SER A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.959A pdb=" N ASN A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 682 through 723 Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.535A pdb=" N ALA A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 797 Processing helix chain 'A' and resid 804 through 826 Processing helix chain 'A' and resid 842 through 861 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 874 through 886 removed outlier: 3.558A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 907 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151 removed outlier: 4.586A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 4.586A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 182 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 226 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP A 180 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 228 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA A 178 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY A 230 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE A 176 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 595 removed outlier: 3.667A pdb=" N TYR A 618 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 347 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE A 569 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 349 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 639 " --> pdb=" O ILE A 657 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 659 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 641 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.911A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA A 462 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU A 451 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A 464 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.911A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A 362 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 545 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 364 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS A 490 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 538 " --> pdb=" O CYS A 490 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 492 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLY A 540 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLN A 494 " --> pdb=" O GLY A 540 " (cutoff:3.500A) removed outlier: 13.890A pdb=" N VAL A 542 " --> pdb=" O GLN A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 417 435 hydrogen bonds defined for protein. 1257 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: 2.26 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2224 1.34 - 1.46: 1402 1.46 - 1.58: 3235 1.58 - 1.70: 1 1.70 - 1.82: 88 Bond restraints: 6950 Sorted by residual: bond pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.786 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F4 ALF A1002 " pdb="AL ALF A1002 " ideal model delta sigma weight residual 1.686 1.784 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" CB PRO A 453 " pdb=" CG PRO A 453 " ideal model delta sigma weight residual 1.492 1.649 -0.157 5.00e-02 4.00e+02 9.85e+00 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.26: 9405 14.26 - 28.52: 4 28.52 - 42.77: 0 42.77 - 57.03: 0 57.03 - 71.29: 2 Bond angle restraints: 9411 Sorted by residual: angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F2 ALF A1002 " ideal model delta sigma weight residual 108.68 179.97 -71.29 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 109.63 179.94 -70.31 3.00e+00 1.11e-01 5.49e+02 angle pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" CD PRO A 453 " ideal model delta sigma weight residual 112.00 102.25 9.75 1.40e+00 5.10e-01 4.85e+01 angle pdb=" F2 ALF A1002 " pdb="AL ALF A1002 " pdb=" F4 ALF A1002 " ideal model delta sigma weight residual 110.21 90.00 20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF A1002 " pdb="AL ALF A1002 " pdb=" F3 ALF A1002 " ideal model delta sigma weight residual 109.69 89.98 19.71 3.00e+00 1.11e-01 4.32e+01 ... (remaining 9406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3675 17.95 - 35.90: 439 35.90 - 53.85: 111 53.85 - 71.79: 17 71.79 - 89.74: 6 Dihedral angle restraints: 4248 sinusoidal: 1676 harmonic: 2572 Sorted by residual: dihedral pdb=" CA ASN A 724 " pdb=" C ASN A 724 " pdb=" N PHE A 725 " pdb=" CA PHE A 725 " ideal model delta harmonic sigma weight residual 180.00 153.42 26.58 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB MET A 219 " pdb=" CG MET A 219 " pdb=" SD MET A 219 " pdb=" CE MET A 219 " ideal model delta sinusoidal sigma weight residual -60.00 -1.30 -58.70 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ILE A 65 " pdb=" CB ILE A 65 " pdb=" CG1 ILE A 65 " pdb=" CD1 ILE A 65 " ideal model delta sinusoidal sigma weight residual 60.00 116.29 -56.29 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 755 0.031 - 0.062: 233 0.062 - 0.092: 95 0.092 - 0.123: 44 0.123 - 0.154: 4 Chirality restraints: 1131 Sorted by residual: chirality pdb=" CA PHE A 702 " pdb=" N PHE A 702 " pdb=" C PHE A 702 " pdb=" CB PHE A 702 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA VAL A 156 " pdb=" N VAL A 156 " pdb=" C VAL A 156 " pdb=" CB VAL A 156 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CB ILE A 711 " pdb=" CA ILE A 711 " pdb=" CG1 ILE A 711 " pdb=" CG2 ILE A 711 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1128 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 452 " 0.053 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 453 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 135 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 136 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 157 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.024 5.00e-02 4.00e+02 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 89 2.66 - 3.22: 6343 3.22 - 3.78: 10777 3.78 - 4.34: 13799 4.34 - 4.90: 23415 Nonbonded interactions: 54423 Sorted by model distance: nonbonded pdb=" OD1 ASP A 644 " pdb="MG MG A1001 " model vdw 2.094 2.170 nonbonded pdb=" O ASP A 350 " pdb=" OG1 THR A 354 " model vdw 2.159 3.040 nonbonded pdb=" O SER A 124 " pdb=" OG SER A 124 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP A 350 " pdb="MG MG A1001 " model vdw 2.263 2.170 nonbonded pdb=" OD1 ASP A 603 " pdb=" N VAL A 604 " model vdw 2.280 3.120 ... (remaining 54418 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.340 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.004 0.157 6950 Z= 0.235 Angle : 1.249 71.291 9411 Z= 0.488 Chirality : 0.039 0.154 1131 Planarity : 0.005 0.076 1189 Dihedral : 16.533 89.742 2584 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 0.13 % Allowed : 23.05 % Favored : 76.82 % 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: 1.91 (0.29), residues: 891 helix: 2.54 (0.24), residues: 477 sheet: 0.15 (0.49), residues: 115 loop : -0.37 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.001 0.000 HIS A 467 PHE 0.025 0.001 PHE A 702 TYR 0.004 0.000 TYR A 587 ARG 0.010 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 492 THR cc_start: 0.7855 (p) cc_final: 0.7548 (t) REVERT: A 504 GLN cc_start: 0.7328 (tp40) cc_final: 0.6573 (tp40) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1714 time to fit residues: 27.8819 Evaluate side-chains 107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 149 HIS A 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132429 restraints weight = 10353.254| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.95 r_work: 0.3628 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6950 Z= 0.229 Angle : 0.579 8.845 9411 Z= 0.300 Chirality : 0.043 0.158 1131 Planarity : 0.005 0.046 1189 Dihedral : 3.770 18.851 941 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 2.73 % Allowed : 21.22 % Favored : 76.04 % 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: 1.70 (0.29), residues: 891 helix: 2.32 (0.23), residues: 488 sheet: -0.04 (0.54), residues: 91 loop : -0.43 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 60 HIS 0.003 0.001 HIS A 467 PHE 0.021 0.002 PHE A 702 TYR 0.005 0.001 TYR A 397 ARG 0.005 0.001 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.603 Fit side-chains REVERT: A 29 LEU cc_start: 0.8445 (mt) cc_final: 0.8176 (mt) REVERT: A 55 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7688 (mtp180) REVERT: A 492 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7686 (t) REVERT: A 716 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8333 (tp) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.1825 time to fit residues: 34.6703 Evaluate side-chains 135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain A residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 605 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.149184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125831 restraints weight = 10417.239| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.96 r_work: 0.3532 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6950 Z= 0.197 Angle : 0.534 6.887 9411 Z= 0.278 Chirality : 0.041 0.156 1131 Planarity : 0.005 0.043 1189 Dihedral : 3.801 18.051 941 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 3.52 % Allowed : 21.88 % Favored : 74.61 % 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: 1.72 (0.29), residues: 891 helix: 2.36 (0.23), residues: 486 sheet: 0.06 (0.54), residues: 96 loop : -0.48 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.002 0.001 HIS A 140 PHE 0.021 0.002 PHE A 702 TYR 0.006 0.001 TYR A 860 ARG 0.005 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7759 (mtm110) REVERT: A 81 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8500 (t0) REVERT: A 167 ASP cc_start: 0.7447 (t0) cc_final: 0.7158 (t0) REVERT: A 492 THR cc_start: 0.7971 (p) cc_final: 0.7711 (t) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.1997 time to fit residues: 39.9430 Evaluate side-chains 141 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 703 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119632 restraints weight = 10278.773| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.85 r_work: 0.3389 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6950 Z= 0.184 Angle : 0.541 9.532 9411 Z= 0.278 Chirality : 0.041 0.152 1131 Planarity : 0.005 0.047 1189 Dihedral : 3.802 17.896 941 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.65 % Allowed : 22.66 % Favored : 73.70 % 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: 1.67 (0.29), residues: 891 helix: 2.29 (0.23), residues: 488 sheet: -0.00 (0.54), residues: 96 loop : -0.45 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 795 HIS 0.006 0.001 HIS A 149 PHE 0.026 0.002 PHE A 702 TYR 0.009 0.001 TYR A 587 ARG 0.008 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.784 Fit side-chains REVERT: A 29 LEU cc_start: 0.8449 (mt) cc_final: 0.8244 (mt) REVERT: A 81 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 167 ASP cc_start: 0.7367 (t0) cc_final: 0.7106 (t0) REVERT: A 174 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (tpt-90) REVERT: A 331 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8835 (mm) REVERT: A 492 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7703 (t) REVERT: A 742 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7367 (t0) outliers start: 28 outliers final: 15 residues processed: 143 average time/residue: 0.1990 time to fit residues: 37.7832 Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 804 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.0270 chunk 53 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 60 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.144243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118102 restraints weight = 10547.672| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.29 r_work: 0.3409 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6950 Z= 0.144 Angle : 0.520 10.032 9411 Z= 0.270 Chirality : 0.040 0.152 1131 Planarity : 0.004 0.047 1189 Dihedral : 3.720 16.631 941 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.04 % Allowed : 22.40 % Favored : 73.57 % 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: 1.74 (0.29), residues: 891 helix: 2.35 (0.23), residues: 488 sheet: -0.02 (0.55), residues: 96 loop : -0.41 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.024 0.001 PHE A 702 TYR 0.005 0.001 TYR A 587 ARG 0.006 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.776 Fit side-chains REVERT: A 81 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 123 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8124 (tpp-160) REVERT: A 126 LYS cc_start: 0.6594 (mmtm) cc_final: 0.6389 (pttt) REVERT: A 331 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (mm) REVERT: A 492 THR cc_start: 0.7921 (p) cc_final: 0.7648 (t) REVERT: A 679 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7751 (t0) REVERT: A 742 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7142 (t0) outliers start: 31 outliers final: 19 residues processed: 138 average time/residue: 0.1877 time to fit residues: 35.1756 Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 0.0770 chunk 42 optimal weight: 0.0670 chunk 81 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120115 restraints weight = 10668.080| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.20 r_work: 0.3446 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6950 Z= 0.133 Angle : 0.516 10.528 9411 Z= 0.265 Chirality : 0.040 0.154 1131 Planarity : 0.004 0.047 1189 Dihedral : 3.635 17.331 941 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.17 % Allowed : 22.01 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.29), residues: 891 helix: 2.41 (0.23), residues: 488 sheet: -0.07 (0.54), residues: 96 loop : -0.33 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 795 HIS 0.006 0.001 HIS A 149 PHE 0.025 0.001 PHE A 702 TYR 0.005 0.001 TYR A 587 ARG 0.007 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.776 Fit side-chains REVERT: A 85 MET cc_start: 0.7108 (mmt) cc_final: 0.6835 (mmt) REVERT: A 123 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8147 (tpp-160) REVERT: A 174 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8316 (tpt-90) REVERT: A 492 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 742 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7163 (t0) outliers start: 32 outliers final: 21 residues processed: 135 average time/residue: 0.2108 time to fit residues: 37.6185 Evaluate side-chains 134 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114778 restraints weight = 10548.510| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.27 r_work: 0.3418 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6950 Z= 0.182 Angle : 0.537 11.221 9411 Z= 0.275 Chirality : 0.041 0.157 1131 Planarity : 0.005 0.046 1189 Dihedral : 3.717 15.613 941 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.95 % Allowed : 21.61 % Favored : 73.44 % 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: 1.72 (0.29), residues: 891 helix: 2.33 (0.23), residues: 488 sheet: -0.07 (0.54), residues: 96 loop : -0.39 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.021 0.002 PHE A 702 TYR 0.005 0.001 TYR A 587 ARG 0.009 0.001 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.738 Fit side-chains REVERT: A 81 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8272 (t0) REVERT: A 85 MET cc_start: 0.7147 (mmt) cc_final: 0.6840 (mmt) REVERT: A 382 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8817 (pt0) REVERT: A 412 ASN cc_start: 0.8103 (m-40) cc_final: 0.7810 (m110) REVERT: A 461 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8042 (ttp) REVERT: A 492 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7732 (t) outliers start: 38 outliers final: 26 residues processed: 145 average time/residue: 0.2704 time to fit residues: 50.9996 Evaluate side-chains 140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110271 restraints weight = 10526.705| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.25 r_work: 0.3350 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6950 Z= 0.273 Angle : 0.597 12.639 9411 Z= 0.307 Chirality : 0.043 0.170 1131 Planarity : 0.005 0.046 1189 Dihedral : 3.976 15.469 941 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.30 % Allowed : 22.53 % Favored : 73.18 % 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: 1.49 (0.29), residues: 891 helix: 2.11 (0.23), residues: 488 sheet: -0.16 (0.54), residues: 97 loop : -0.44 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.022 0.002 PHE A 702 TYR 0.007 0.001 TYR A 510 ARG 0.008 0.001 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8378 (t0) REVERT: A 382 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: A 412 ASN cc_start: 0.8288 (m-40) cc_final: 0.7946 (m110) REVERT: A 461 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.7996 (ttp) REVERT: A 903 GLU cc_start: 0.7774 (mp0) cc_final: 0.7505 (mp0) outliers start: 33 outliers final: 23 residues processed: 142 average time/residue: 0.1868 time to fit residues: 36.9460 Evaluate side-chains 138 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 679 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 81 optimal weight: 0.0470 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 829 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115072 restraints weight = 10471.965| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.23 r_work: 0.3416 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6950 Z= 0.152 Angle : 0.552 13.869 9411 Z= 0.280 Chirality : 0.041 0.159 1131 Planarity : 0.004 0.049 1189 Dihedral : 3.826 16.455 941 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.52 % Allowed : 23.05 % Favored : 73.44 % 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: 1.71 (0.29), residues: 891 helix: 2.32 (0.23), residues: 487 sheet: -0.04 (0.54), residues: 97 loop : -0.39 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 795 HIS 0.006 0.001 HIS A 149 PHE 0.023 0.001 PHE A 702 TYR 0.005 0.001 TYR A 493 ARG 0.007 0.001 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.710 Fit side-chains REVERT: A 81 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8356 (t0) REVERT: A 382 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8727 (pt0) REVERT: A 412 ASN cc_start: 0.7979 (m-40) cc_final: 0.7685 (m110) REVERT: A 461 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: A 492 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7713 (t) REVERT: A 742 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7285 (t0) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.1674 time to fit residues: 31.4984 Evaluate side-chains 138 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113057 restraints weight = 10683.906| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.27 r_work: 0.3386 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6950 Z= 0.202 Angle : 0.583 13.500 9411 Z= 0.296 Chirality : 0.042 0.176 1131 Planarity : 0.005 0.049 1189 Dihedral : 3.867 18.471 941 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.52 % Allowed : 23.44 % Favored : 73.05 % 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: 1.66 (0.29), residues: 891 helix: 2.28 (0.23), residues: 487 sheet: -0.08 (0.55), residues: 97 loop : -0.42 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 795 HIS 0.006 0.001 HIS A 149 PHE 0.022 0.002 PHE A 702 TYR 0.005 0.001 TYR A 587 ARG 0.008 0.001 ARG A 842 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8343 (t0) REVERT: A 382 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: A 412 ASN cc_start: 0.8079 (m-40) cc_final: 0.7791 (m110) REVERT: A 461 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: A 492 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7723 (t) outliers start: 27 outliers final: 21 residues processed: 131 average time/residue: 0.1806 time to fit residues: 32.6352 Evaluate side-chains 133 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110630 restraints weight = 10618.588| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.26 r_work: 0.3367 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6950 Z= 0.225 Angle : 0.592 13.278 9411 Z= 0.302 Chirality : 0.042 0.173 1131 Planarity : 0.005 0.048 1189 Dihedral : 3.960 19.084 941 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.65 % Allowed : 23.31 % Favored : 73.05 % 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: 1.58 (0.29), residues: 891 helix: 2.22 (0.23), residues: 487 sheet: -0.10 (0.55), residues: 97 loop : -0.46 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 795 HIS 0.006 0.001 HIS A 149 PHE 0.024 0.002 PHE A 818 TYR 0.006 0.001 TYR A 587 ARG 0.007 0.001 ARG A 473 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4089.38 seconds wall clock time: 73 minutes 17.70 seconds (4397.70 seconds total)