Starting phenix.real_space_refine on Tue Nov 14 06:35:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lle_0912/11_2023/6lle_0912_updated.pdb" } resolution = 2.9 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= 0.020 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 Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 5038 2.51 5 N 1319 2.21 5 O 1495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ASP 456": "OD1" <-> "OD2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A TYR 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 907": "OE1" <-> "OE2" Residue "A ASP 980": "OD1" <-> "OD2" Residue "A GLU 992": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7916 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7916 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'peptide': 1020, 'undetermined': 4} Link IDs: {'PTRANS': 46, 'TRANS': 973, None: 4} Not linked: pdbres="SER A1042 " pdbres="ACP A2001 " Not linked: pdbres="ACP A2001 " pdbres=" MG A2002 " Not linked: pdbres=" MG A2002 " pdbres=" CA A2003 " Not linked: pdbres=" CA A2003 " pdbres=" CA A2004 " Chain breaks: 2 Time building chain proxies: 4.70, per 1000 atoms: 0.59 Number of scatterers: 7916 At special positions: 0 Unit cell: (93.375, 78.435, 141.93, 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) Ca 2 19.99 S 58 16.00 P 3 15.00 Mg 1 11.99 O 1495 8.00 N 1319 7.00 C 5038 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 - 3.50 Amino acid : False - 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 45.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.874A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.859A pdb=" N GLN A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 75 Processing helix chain 'A' and resid 89 through 119 removed outlier: 3.992A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 248 through 273 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 288 through 306 removed outlier: 3.512A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 removed outlier: 3.642A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 409 through 419 Processing helix chain 'A' and resid 440 through 452 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.602A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.558A pdb=" N MET A 545 " --> pdb=" O LYS A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 580 through 585 removed outlier: 4.110A pdb=" N ILE A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 removed outlier: 3.511A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 671 removed outlier: 4.005A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.640A pdb=" N VAL A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 removed outlier: 3.513A pdb=" N LYS A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 739 through 780 removed outlier: 4.418A pdb=" N VAL A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS A 773 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 780 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 798 Processing helix chain 'A' and resid 801 through 808 removed outlier: 4.116A pdb=" N LEU A 806 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 807 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.683A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 872 through 874 No H-bonds generated for 'chain 'A' and resid 872 through 874' Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 893 through 914 removed outlier: 3.640A pdb=" N LEU A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 913 " --> pdb=" O CYS A 909 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 Processing helix chain 'A' and resid 953 through 956 No H-bonds generated for 'chain 'A' and resid 953 through 956' Processing helix chain 'A' and resid 963 through 989 removed outlier: 3.641A pdb=" N MET A 968 " --> pdb=" O THR A 964 " (cutoff:3.500A) Proline residue: A 975 - end of helix removed outlier: 3.915A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.638A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.556A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.610A pdb=" N ILE A 715 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 424 through 428 Processing sheet with id= D, first strand: chain 'A' and resid 376 through 383 removed outlier: 5.747A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.749A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.395A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 174 through 176 removed outlier: 5.791A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 867 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: 2.73 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2592 1.35 - 1.48: 1830 1.48 - 1.61: 3546 1.61 - 1.73: 4 1.73 - 1.86: 92 Bond restraints: 8064 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.617 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.306 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.299 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8059 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.67: 248 106.67 - 113.50: 4580 113.50 - 120.34: 2979 120.34 - 127.17: 3050 127.17 - 134.00: 94 Bond angle restraints: 10951 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 108.99 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.24 -12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 109.22 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 109.04 10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.80 10.15 3.00e+00 1.11e-01 1.14e+01 ... (remaining 10946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 4672 23.50 - 47.00: 171 47.00 - 70.49: 19 70.49 - 93.99: 6 93.99 - 117.49: 1 Dihedral angle restraints: 4869 sinusoidal: 1923 harmonic: 2946 Sorted by residual: dihedral pdb=" CA ILE A 153 " pdb=" C ILE A 153 " pdb=" N ALA A 154 " pdb=" CA ALA A 154 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 68.74 -117.49 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CA VAL A 949 " pdb=" C VAL A 949 " pdb=" N GLU A 950 " pdb=" CA GLU A 950 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1184 0.079 - 0.158: 97 0.158 - 0.237: 1 0.237 - 0.316: 0 0.316 - 0.395: 1 Chirality restraints: 1283 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB ILE A 153 " pdb=" CA ILE A 153 " pdb=" CG1 ILE A 153 " pdb=" CG2 ILE A 153 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1280 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A1017 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 661 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 662 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 975 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.017 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 94 2.62 - 3.19: 7043 3.19 - 3.76: 12358 3.76 - 4.33: 17775 4.33 - 4.90: 29059 Nonbonded interactions: 66329 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.050 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.114 2.170 nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.170 2.170 nonbonded pdb=" O3G ACP A2001 " pdb="MG MG A2002 " model vdw 2.171 2.170 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.192 2.170 ... (remaining 66324 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: 0.260 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: 1.480 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.120 Find NCS groups from input model: 0.220 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 8064 Z= 0.307 Angle : 0.632 15.238 10951 Z= 0.315 Chirality : 0.043 0.395 1283 Planarity : 0.004 0.036 1390 Dihedral : 12.591 117.490 2959 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -1.87 (0.24), residues: 1014 helix: -0.83 (0.22), residues: 472 sheet: -1.09 (0.47), residues: 104 loop : -1.62 (0.27), residues: 438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.998 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 1.2661 time to fit residues: 245.0591 Evaluate side-chains 124 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 190 HIS A 251 GLN A 275 ASN A 469 ASN A 817 ASN A 913 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8064 Z= 0.248 Angle : 0.541 6.096 10951 Z= 0.278 Chirality : 0.043 0.160 1283 Planarity : 0.005 0.035 1390 Dihedral : 6.407 139.891 1082 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.44 % Allowed : 12.83 % Favored : 83.73 % 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: -0.80 (0.26), residues: 1014 helix: 0.16 (0.24), residues: 477 sheet: -0.91 (0.43), residues: 114 loop : -1.12 (0.29), residues: 423 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.897 Fit side-chains outliers start: 30 outliers final: 13 residues processed: 135 average time/residue: 1.2107 time to fit residues: 173.5810 Evaluate side-chains 124 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1300 time to fit residues: 1.7453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.0000 chunk 100 optimal weight: 0.0670 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8064 Z= 0.136 Angle : 0.484 7.153 10951 Z= 0.245 Chirality : 0.040 0.190 1283 Planarity : 0.004 0.033 1390 Dihedral : 6.048 131.414 1082 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.32 % Allowed : 15.12 % Favored : 81.56 % 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: -0.14 (0.26), residues: 1014 helix: 0.78 (0.24), residues: 470 sheet: -0.59 (0.44), residues: 114 loop : -0.85 (0.30), residues: 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.155 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 148 average time/residue: 1.1453 time to fit residues: 180.5483 Evaluate side-chains 134 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 1.4003 time to fit residues: 4.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 472 ASN A 643 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8064 Z= 0.216 Angle : 0.521 7.333 10951 Z= 0.263 Chirality : 0.042 0.185 1283 Planarity : 0.004 0.030 1390 Dihedral : 6.289 138.173 1082 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.44 % Allowed : 16.61 % Favored : 79.95 % 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: -0.06 (0.26), residues: 1014 helix: 0.77 (0.24), residues: 478 sheet: -0.47 (0.44), residues: 115 loop : -0.77 (0.31), residues: 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.870 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 143 average time/residue: 1.1277 time to fit residues: 171.8621 Evaluate side-chains 136 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.7420 time to fit residues: 3.7323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8064 Z= 0.177 Angle : 0.506 7.623 10951 Z= 0.255 Chirality : 0.041 0.175 1283 Planarity : 0.004 0.030 1390 Dihedral : 6.207 135.976 1082 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.78 % Allowed : 16.15 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1014 helix: 0.85 (0.24), residues: 482 sheet: -0.28 (0.45), residues: 113 loop : -0.80 (0.30), residues: 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.158 Fit side-chains outliers start: 33 outliers final: 22 residues processed: 143 average time/residue: 1.1207 time to fit residues: 171.0690 Evaluate side-chains 134 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.4046 time to fit residues: 4.0681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 643 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8064 Z= 0.137 Angle : 0.483 8.026 10951 Z= 0.243 Chirality : 0.040 0.145 1283 Planarity : 0.004 0.029 1390 Dihedral : 5.798 126.085 1082 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.09 % Allowed : 17.75 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1014 helix: 1.04 (0.24), residues: 485 sheet: -0.22 (0.47), residues: 115 loop : -0.70 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.881 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 1.1461 time to fit residues: 183.4090 Evaluate side-chains 139 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 1.0735 time to fit residues: 3.7162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8064 Z= 0.205 Angle : 0.529 9.924 10951 Z= 0.264 Chirality : 0.041 0.183 1283 Planarity : 0.004 0.029 1390 Dihedral : 5.790 127.879 1082 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.09 % Allowed : 18.56 % Favored : 78.35 % 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: 0.29 (0.27), residues: 1014 helix: 1.01 (0.24), residues: 484 sheet: -0.04 (0.46), residues: 114 loop : -0.63 (0.31), residues: 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.997 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 143 average time/residue: 1.0793 time to fit residues: 165.1628 Evaluate side-chains 134 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2138 time to fit residues: 1.5769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 0.0170 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8064 Z= 0.160 Angle : 0.511 10.775 10951 Z= 0.255 Chirality : 0.041 0.173 1283 Planarity : 0.004 0.029 1390 Dihedral : 5.457 119.333 1082 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.98 % Allowed : 19.13 % Favored : 77.89 % 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: 0.45 (0.27), residues: 1014 helix: 1.17 (0.24), residues: 479 sheet: 0.02 (0.46), residues: 114 loop : -0.56 (0.31), residues: 421 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.981 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 1.1870 time to fit residues: 181.0560 Evaluate side-chains 135 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 1.6195 time to fit residues: 2.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8064 Z= 0.166 Angle : 0.516 11.339 10951 Z= 0.257 Chirality : 0.041 0.155 1283 Planarity : 0.004 0.032 1390 Dihedral : 5.349 117.353 1082 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.63 % Allowed : 19.36 % Favored : 78.01 % 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: 0.51 (0.27), residues: 1014 helix: 1.21 (0.24), residues: 478 sheet: 0.11 (0.47), residues: 114 loop : -0.55 (0.31), residues: 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.115 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 1.1321 time to fit residues: 169.4170 Evaluate side-chains 134 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1221 time to fit residues: 1.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 8 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8064 Z= 0.183 Angle : 0.530 11.915 10951 Z= 0.263 Chirality : 0.041 0.161 1283 Planarity : 0.004 0.031 1390 Dihedral : 5.354 118.879 1082 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.95 % Allowed : 19.70 % Favored : 78.35 % 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: 0.53 (0.27), residues: 1014 helix: 1.20 (0.24), residues: 479 sheet: 0.12 (0.47), residues: 114 loop : -0.51 (0.31), residues: 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.985 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 139 average time/residue: 1.1864 time to fit residues: 175.9095 Evaluate side-chains 133 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.3576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.0020 chunk 33 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 0.0370 overall best weight: 0.3666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.116663 restraints weight = 8209.712| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.58 r_work: 0.2992 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8064 Z= 0.142 Angle : 0.523 11.801 10951 Z= 0.260 Chirality : 0.040 0.137 1283 Planarity : 0.004 0.031 1390 Dihedral : 5.178 115.866 1082 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.83 % Allowed : 20.62 % Favored : 77.55 % 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: 0.63 (0.27), residues: 1014 helix: 1.31 (0.24), residues: 482 sheet: 0.07 (0.48), residues: 115 loop : -0.47 (0.31), residues: 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3411.91 seconds wall clock time: 61 minutes 28.06 seconds (3688.06 seconds total)