Starting phenix.real_space_refine on Thu Nov 14 17:43:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_35780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_35780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_35780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_35780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwu_35780/11_2024/8iwu_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-5513/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: 5.07, per 1000 atoms: 0.74 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: 2.00 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: 1.04 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: 2.77 Time building geometry restraints manager: 2.18 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: 6.580 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 21.070 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- 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 : 0.812 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: 0.1730 time to fit residues: 28.4036 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 : 0.876 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.727 Fit side-chains REVERT: A 29 LEU cc_start: 0.8428 (mt) cc_final: 0.8202 (mt) REVERT: A 55 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7617 (mtp180) REVERT: A 492 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7592 (t) REVERT: A 716 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8358 (tp) outliers start: 21 outliers final: 12 residues processed: 140 average time/residue: 0.1857 time to fit residues: 35.3549 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 : 0.802 ------------------------------------------------------------------------------- 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 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6950 Z= 0.206 Angle : 0.535 6.889 9411 Z= 0.279 Chirality : 0.041 0.160 1131 Planarity : 0.005 0.042 1189 Dihedral : 3.806 18.423 941 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % 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: 0.04 (0.54), residues: 96 loop : -0.47 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.002 0.001 HIS A 58 PHE 0.022 0.002 PHE A 702 TYR 0.006 0.001 TYR A 860 ARG 0.007 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 155 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8602 (t0) REVERT: A 167 ASP cc_start: 0.7187 (t0) cc_final: 0.6908 (t0) REVERT: A 492 THR cc_start: 0.7889 (p) cc_final: 0.7650 (t) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.1994 time to fit residues: 39.6379 Evaluate side-chains 140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 721 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6950 Z= 0.271 Angle : 0.586 8.788 9411 Z= 0.304 Chirality : 0.042 0.161 1131 Planarity : 0.005 0.048 1189 Dihedral : 3.984 17.655 941 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.69 % Allowed : 22.01 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 891 helix: 2.14 (0.23), residues: 493 sheet: -0.08 (0.54), residues: 96 loop : -0.61 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.025 0.002 PHE A 702 TYR 0.009 0.001 TYR A 587 ARG 0.006 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 160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8628 (t0) outliers start: 36 outliers final: 21 residues processed: 148 average time/residue: 0.2012 time to fit residues: 40.2535 Evaluate side-chains 135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 394 HIS Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.2678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2839 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= 0.140 Angle : 0.519 10.608 9411 Z= 0.269 Chirality : 0.040 0.145 1131 Planarity : 0.004 0.049 1189 Dihedral : 3.810 15.602 941 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.39 % Allowed : 22.27 % Favored : 74.35 % 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: 1.69 (0.29), residues: 891 helix: 2.31 (0.23), residues: 493 sheet: 0.07 (0.57), residues: 90 loop : -0.51 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.025 0.001 PHE A 702 TYR 0.006 0.001 TYR A 493 ARG 0.007 0.001 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 147 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8555 (t0) REVERT: A 123 ARG cc_start: 0.8347 (tpp80) cc_final: 0.8052 (tpp-160) REVERT: A 382 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8563 (pt0) REVERT: A 492 THR cc_start: 0.7847 (p) cc_final: 0.7581 (t) REVERT: A 742 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7268 (t0) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.1886 time to fit residues: 35.8629 Evaluate side-chains 130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 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 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 742 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 804 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6950 Z= 0.231 Angle : 0.562 7.621 9411 Z= 0.292 Chirality : 0.042 0.171 1131 Planarity : 0.005 0.046 1189 Dihedral : 3.910 15.650 941 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.69 % Allowed : 21.48 % 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: 1.52 (0.29), residues: 891 helix: 2.20 (0.23), residues: 493 sheet: -0.13 (0.56), residues: 90 loop : -0.59 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.022 0.002 PHE A 702 TYR 0.006 0.001 TYR A 587 ARG 0.007 0.001 ARG A 473 *********************** 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 148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.808 Fit side-chains REVERT: A 81 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8605 (t0) REVERT: A 382 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: A 461 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.7715 (ttp) outliers start: 36 outliers final: 24 residues processed: 137 average time/residue: 0.1834 time to fit residues: 34.6335 Evaluate side-chains 135 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 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 679 ASP Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 770 ILE 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 62 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6950 Z= 0.183 Angle : 0.539 6.828 9411 Z= 0.283 Chirality : 0.041 0.157 1131 Planarity : 0.005 0.048 1189 Dihedral : 3.870 14.810 941 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.78 % Allowed : 22.27 % Favored : 73.96 % 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: 1.55 (0.29), residues: 891 helix: 2.20 (0.23), residues: 493 sheet: -0.08 (0.57), residues: 90 loop : -0.55 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.023 0.001 PHE A 702 TYR 0.005 0.001 TYR A 587 ARG 0.007 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 139 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.765 Fit side-chains REVERT: A 81 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8565 (t0) REVERT: A 382 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: A 492 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7633 (t) REVERT: A 742 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7416 (t0) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.1723 time to fit residues: 31.0301 Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6950 Z= 0.225 Angle : 0.557 7.027 9411 Z= 0.293 Chirality : 0.042 0.161 1131 Planarity : 0.005 0.047 1189 Dihedral : 3.950 15.132 941 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.43 % Allowed : 22.40 % 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: 1.52 (0.29), residues: 891 helix: 2.18 (0.23), residues: 487 sheet: -0.17 (0.54), residues: 97 loop : -0.48 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 795 HIS 0.006 0.001 HIS A 53 PHE 0.022 0.002 PHE A 702 TYR 0.007 0.001 TYR A 587 ARG 0.007 0.001 ARG A 842 *********************** 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 148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.867 Fit side-chains REVERT: A 81 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8530 (t0) REVERT: A 382 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8551 (pt0) REVERT: A 461 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7727 (ttp) REVERT: A 742 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7453 (t0) outliers start: 34 outliers final: 26 residues processed: 137 average time/residue: 0.1779 time to fit residues: 34.5195 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 : 0.802 ------------------------------------------------------------------------------- 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 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 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 492 THR Chi-restraints excluded: chain A residue 533 LEU 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 703 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3536 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= 0.190 Angle : 0.551 6.847 9411 Z= 0.290 Chirality : 0.041 0.169 1131 Planarity : 0.005 0.048 1189 Dihedral : 3.927 15.304 941 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.30 % Allowed : 23.05 % Favored : 72.66 % 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: 1.56 (0.29), residues: 891 helix: 2.18 (0.23), residues: 493 sheet: -0.13 (0.54), residues: 97 loop : -0.48 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 795 HIS 0.007 0.001 HIS A 53 PHE 0.023 0.002 PHE A 702 TYR 0.006 0.001 TYR A 587 ARG 0.007 0.000 ARG A 468 *********************** 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 148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.919 Fit side-chains REVERT: A 81 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8530 (t0) REVERT: A 123 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7944 (tpp-160) REVERT: A 382 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (pt0) REVERT: A 461 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.7757 (ttp) REVERT: A 742 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7471 (t0) outliers start: 33 outliers final: 26 residues processed: 137 average time/residue: 0.1966 time to fit residues: 38.0515 Evaluate side-chains 141 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 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 492 THR Chi-restraints excluded: chain A residue 533 LEU 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 703 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6950 Z= 0.232 Angle : 0.576 7.421 9411 Z= 0.303 Chirality : 0.042 0.173 1131 Planarity : 0.005 0.047 1189 Dihedral : 3.990 17.144 941 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.56 % Allowed : 22.92 % Favored : 72.53 % 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: 1.45 (0.29), residues: 891 helix: 2.13 (0.23), residues: 488 sheet: -0.20 (0.54), residues: 97 loop : -0.54 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.028 0.002 PHE A 880 TYR 0.006 0.001 TYR A 587 ARG 0.006 0.000 ARG A 468 ********************** 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 147 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.824 Fit side-chains REVERT: A 81 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8548 (t0) REVERT: A 123 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7966 (tpp-160) REVERT: A 382 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8539 (pt0) REVERT: A 461 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: A 742 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7560 (t0) outliers start: 35 outliers final: 29 residues processed: 135 average time/residue: 0.1863 time to fit residues: 34.8001 Evaluate side-chains 143 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 448 ARG 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 533 LEU 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 770 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 876 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.136666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110051 restraints weight = 10474.937| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.24 r_work: 0.3357 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.272 6950 Z= 0.432 Angle : 1.004 59.200 9411 Z= 0.594 Chirality : 0.042 0.166 1131 Planarity : 0.005 0.047 1189 Dihedral : 3.983 17.060 941 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.43 % Allowed : 23.05 % Favored : 72.53 % Cbeta Deviations : 0.12 % 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: 1.45 (0.29), residues: 891 helix: 2.13 (0.23), residues: 488 sheet: -0.20 (0.54), residues: 97 loop : -0.54 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 795 HIS 0.005 0.001 HIS A 149 PHE 0.025 0.002 PHE A 880 TYR 0.005 0.001 TYR A 587 ARG 0.005 0.000 ARG A 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.08 seconds wall clock time: 37 minutes 39.17 seconds (2259.17 seconds total)