Starting phenix.real_space_refine on Mon Mar 11 08:11:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yah_33712/03_2024/7yah_33712_updated.pdb" } resolution = 3.12 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= 0.005 sd= 0.060 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4872 2.51 5 N 1285 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 871": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7666 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6692 Classifications: {'peptide': 876} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 34, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.65 Number of scatterers: 7666 At special positions: 0 Unit cell: (84.71, 80.77, 134.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1450 8.00 N 1285 7.00 C 4872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.03 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: 3.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 8 sheets defined 45.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.899A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 100 through 134 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 257 through 287 removed outlier: 3.500A pdb=" N ASP A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 308 through 327 removed outlier: 4.296A pdb=" N ILE A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.030A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 341 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.631A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 removed outlier: 3.553A pdb=" N GLN A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.676A pdb=" N ALA A 649 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 650 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 651 " --> pdb=" O ASP A 648 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 653 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 722 removed outlier: 3.545A pdb=" N ILE A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 744 through 750 removed outlier: 3.850A pdb=" N LEU A 749 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 798 Processing helix chain 'A' and resid 805 through 824 Processing helix chain 'A' and resid 833 through 836 No H-bonds generated for 'chain 'A' and resid 833 through 836' Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 903 removed outlier: 4.490A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.194A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 231 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU A 175 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 330 through 332 removed outlier: 7.095A pdb=" N VAL A 346 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR A 642 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 348 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SER A 565 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER A 349 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS A 567 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.738A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.105A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.033A pdb=" N ASP A 180 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 592 through 595 removed outlier: 7.464A pdb=" N VAL A 594 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE A 617 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.707A pdb=" N ASP C 105 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 146 through 149 removed outlier: 4.700A pdb=" N LEU C 146 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 82 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 2.83 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1444 1.33 - 1.45: 1777 1.45 - 1.57: 4480 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 7793 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.793 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.579 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C LEU A 335 " pdb=" N PRO A 336 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 1.00e+01 bond pdb=" CA SER A 687 " pdb=" CB SER A 687 " ideal model delta sigma weight residual 1.528 1.481 0.048 1.56e-02 4.11e+03 9.28e+00 ... (remaining 7788 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.26: 151 105.26 - 112.48: 4152 112.48 - 119.70: 2578 119.70 - 126.92: 3602 126.92 - 134.14: 72 Bond angle restraints: 10555 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 110.27 14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" N MET A 97 " pdb=" CA MET A 97 " pdb=" C MET A 97 " ideal model delta sigma weight residual 108.17 100.87 7.30 1.85e+00 2.92e-01 1.56e+01 angle pdb=" N MET A 262 " pdb=" CA MET A 262 " pdb=" C MET A 262 " ideal model delta sigma weight residual 112.89 108.09 4.80 1.24e+00 6.50e-01 1.50e+01 angle pdb=" CA MET A 97 " pdb=" C MET A 97 " pdb=" O MET A 97 " ideal model delta sigma weight residual 121.66 117.21 4.45 1.17e+00 7.31e-01 1.45e+01 angle pdb=" C SER A 825 " pdb=" N SER A 826 " pdb=" CA SER A 826 " ideal model delta sigma weight residual 122.54 116.30 6.24 1.65e+00 3.67e-01 1.43e+01 ... (remaining 10550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 4451 26.38 - 52.75: 251 52.75 - 79.13: 26 79.13 - 105.51: 4 105.51 - 131.88: 1 Dihedral angle restraints: 4733 sinusoidal: 1867 harmonic: 2866 Sorted by residual: dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 83.13 -131.88 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA PHE A 861 " pdb=" C PHE A 861 " pdb=" N PRO A 862 " pdb=" CA PRO A 862 " ideal model delta harmonic sigma weight residual 180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" O1B ACP A1001 " pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sinusoidal sigma weight residual -52.82 50.74 -103.56 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 4730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1035 0.065 - 0.130: 180 0.130 - 0.196: 26 0.196 - 0.261: 6 0.261 - 0.326: 1 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA MET A 97 " pdb=" N MET A 97 " pdb=" C MET A 97 " pdb=" CB MET A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA MET A 686 " pdb=" N MET A 686 " pdb=" C MET A 686 " pdb=" CB MET A 686 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA GLN A 99 " pdb=" N GLN A 99 " pdb=" C GLN A 99 " pdb=" CB GLN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1245 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 822 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN A 822 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 822 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 823 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 97 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C MET A 97 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 97 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS A 98 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 260 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C LYS A 260 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS A 260 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 261 " 0.013 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1295 2.76 - 3.30: 7558 3.30 - 3.83: 13168 3.83 - 4.37: 15747 4.37 - 4.90: 26785 Nonbonded interactions: 64553 Sorted by model distance: nonbonded pdb=" OG1 THR A 570 " pdb=" O PHE A 617 " model vdw 2.229 2.440 nonbonded pdb=" O LEU A 884 " pdb=" OG SER A 887 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 352 " pdb=" O3G ACP A1001 " model vdw 2.258 2.440 nonbonded pdb=" O GLY A 395 " pdb=" OG SER A 402 " model vdw 2.260 2.440 nonbonded pdb=" OG SER C 142 " pdb=" OD1 ASP C 144 " model vdw 2.279 2.440 ... (remaining 64548 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: 0.470 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: 2.260 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 7793 Z= 0.396 Angle : 0.841 14.791 10555 Z= 0.504 Chirality : 0.053 0.326 1248 Planarity : 0.005 0.051 1328 Dihedral : 15.971 131.883 2884 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.35 % Allowed : 19.27 % Favored : 80.38 % 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: 0.05 (0.25), residues: 989 helix: 0.33 (0.22), residues: 498 sheet: 0.29 (0.45), residues: 122 loop : -0.27 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 460 HIS 0.002 0.001 HIS C 86 PHE 0.023 0.002 PHE A 57 TYR 0.023 0.002 TYR C 112 ARG 0.013 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.931 Fit side-chains REVERT: A 100 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6195 (t80) outliers start: 3 outliers final: 1 residues processed: 95 average time/residue: 0.1983 time to fit residues: 26.2585 Evaluate side-chains 89 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7793 Z= 0.186 Angle : 0.500 6.572 10555 Z= 0.265 Chirality : 0.040 0.131 1248 Planarity : 0.004 0.046 1328 Dihedral : 8.180 124.092 1094 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.96 % Allowed : 17.97 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 989 helix: 1.25 (0.23), residues: 492 sheet: 0.22 (0.45), residues: 128 loop : -0.15 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 66 HIS 0.001 0.000 HIS C 86 PHE 0.013 0.001 PHE A 812 TYR 0.016 0.001 TYR C 112 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 0.939 Fit side-chains REVERT: A 100 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5822 (t80) outliers start: 25 outliers final: 12 residues processed: 103 average time/residue: 0.1834 time to fit residues: 26.9097 Evaluate side-chains 96 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7793 Z= 0.265 Angle : 0.538 6.537 10555 Z= 0.284 Chirality : 0.041 0.138 1248 Planarity : 0.004 0.057 1328 Dihedral : 8.132 130.502 1094 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.85 % Allowed : 17.14 % 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: 0.76 (0.26), residues: 989 helix: 1.19 (0.23), residues: 495 sheet: 0.14 (0.45), residues: 123 loop : -0.16 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 66 HIS 0.001 0.001 HIS A 624 PHE 0.014 0.002 PHE A 812 TYR 0.013 0.001 TYR C 112 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 89 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6117 (t80) REVERT: A 773 LYS cc_start: 0.7273 (ttpp) cc_final: 0.7054 (ttpp) outliers start: 41 outliers final: 26 residues processed: 115 average time/residue: 0.1698 time to fit residues: 28.2212 Evaluate side-chains 110 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7793 Z= 0.211 Angle : 0.505 6.394 10555 Z= 0.265 Chirality : 0.040 0.131 1248 Planarity : 0.004 0.058 1328 Dihedral : 8.028 126.253 1094 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.61 % Allowed : 18.32 % Favored : 77.07 % 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: 1.06 (0.27), residues: 989 helix: 1.47 (0.23), residues: 488 sheet: 0.25 (0.45), residues: 123 loop : -0.04 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.001 0.000 HIS A 372 PHE 0.024 0.001 PHE A 812 TYR 0.011 0.001 TYR C 112 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 1.007 Fit side-chains REVERT: A 100 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.5832 (t80) outliers start: 39 outliers final: 24 residues processed: 118 average time/residue: 0.1853 time to fit residues: 31.6943 Evaluate side-chains 112 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7793 Z= 0.224 Angle : 0.511 6.986 10555 Z= 0.267 Chirality : 0.040 0.132 1248 Planarity : 0.004 0.058 1328 Dihedral : 7.948 125.710 1092 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.61 % Allowed : 19.39 % Favored : 76.00 % 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: 1.00 (0.27), residues: 989 helix: 1.42 (0.23), residues: 495 sheet: 0.16 (0.45), residues: 124 loop : -0.08 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 66 HIS 0.002 0.000 HIS A 98 PHE 0.023 0.002 PHE A 812 TYR 0.011 0.001 TYR A 696 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 0.879 Fit side-chains REVERT: A 100 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5877 (t80) outliers start: 39 outliers final: 31 residues processed: 112 average time/residue: 0.1640 time to fit residues: 26.7174 Evaluate side-chains 118 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7793 Z= 0.169 Angle : 0.489 6.511 10555 Z= 0.255 Chirality : 0.039 0.132 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.837 122.147 1092 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.26 % Allowed : 19.74 % Favored : 76.00 % 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: 1.23 (0.27), residues: 989 helix: 1.64 (0.23), residues: 495 sheet: 0.30 (0.46), residues: 123 loop : -0.02 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 66 HIS 0.003 0.001 HIS A 140 PHE 0.019 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 0.738 Fit side-chains REVERT: A 100 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5628 (t80) outliers start: 36 outliers final: 27 residues processed: 114 average time/residue: 0.1823 time to fit residues: 29.9979 Evaluate side-chains 113 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN A 829 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7793 Z= 0.163 Angle : 0.490 8.118 10555 Z= 0.253 Chirality : 0.039 0.125 1248 Planarity : 0.004 0.055 1328 Dihedral : 7.788 120.743 1092 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 20.69 % Favored : 75.65 % 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: 1.23 (0.27), residues: 989 helix: 1.67 (0.23), residues: 496 sheet: 0.35 (0.45), residues: 123 loop : -0.10 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS A 149 PHE 0.018 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 0.806 Fit side-chains REVERT: A 100 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5605 (t80) outliers start: 31 outliers final: 23 residues processed: 108 average time/residue: 0.1679 time to fit residues: 26.1872 Evaluate side-chains 104 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7793 Z= 0.210 Angle : 0.526 9.359 10555 Z= 0.270 Chirality : 0.041 0.353 1248 Planarity : 0.004 0.056 1328 Dihedral : 7.848 122.460 1092 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.26 % Allowed : 20.09 % Favored : 75.65 % 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: 1.15 (0.27), residues: 989 helix: 1.56 (0.23), residues: 490 sheet: 0.32 (0.43), residues: 136 loop : -0.05 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.001 0.000 HIS A 149 PHE 0.020 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 0.900 Fit side-chains REVERT: A 100 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5651 (t80) outliers start: 36 outliers final: 32 residues processed: 113 average time/residue: 0.1719 time to fit residues: 28.0087 Evaluate side-chains 114 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 81 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7793 Z= 0.194 Angle : 0.532 14.269 10555 Z= 0.270 Chirality : 0.041 0.339 1248 Planarity : 0.004 0.055 1328 Dihedral : 7.821 121.444 1092 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.37 % Allowed : 20.09 % Favored : 75.53 % 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: 1.18 (0.27), residues: 989 helix: 1.58 (0.23), residues: 489 sheet: 0.37 (0.46), residues: 123 loop : -0.03 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.001 0.000 HIS A 149 PHE 0.019 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5647 (t80) REVERT: A 159 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.5439 (t0) outliers start: 37 outliers final: 30 residues processed: 114 average time/residue: 0.1742 time to fit residues: 28.4945 Evaluate side-chains 115 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 83 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7793 Z= 0.186 Angle : 0.534 16.432 10555 Z= 0.269 Chirality : 0.040 0.333 1248 Planarity : 0.004 0.055 1328 Dihedral : 7.802 120.676 1092 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.14 % Allowed : 20.21 % Favored : 75.65 % 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: 1.22 (0.27), residues: 989 helix: 1.62 (0.23), residues: 487 sheet: 0.39 (0.46), residues: 123 loop : -0.01 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.001 0.000 HIS A 372 PHE 0.019 0.001 PHE A 812 TYR 0.009 0.001 TYR A 696 ARG 0.007 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 0.913 Fit side-chains REVERT: A 100 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.5511 (t80) REVERT: A 159 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.5434 (t0) outliers start: 35 outliers final: 30 residues processed: 116 average time/residue: 0.1728 time to fit residues: 28.8268 Evaluate side-chains 116 residues out of total 849 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 394 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 769 SER Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 153 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.223206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.186485 restraints weight = 7173.683| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.74 r_work: 0.3750 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7793 Z= 0.144 Angle : 0.509 15.419 10555 Z= 0.257 Chirality : 0.040 0.321 1248 Planarity : 0.004 0.053 1328 Dihedral : 7.709 117.579 1092 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.07 % Allowed : 21.28 % Favored : 75.65 % 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: 1.43 (0.27), residues: 989 helix: 1.80 (0.23), residues: 487 sheet: 0.52 (0.46), residues: 123 loop : 0.07 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 460 HIS 0.001 0.000 HIS C 86 PHE 0.017 0.001 PHE A 812 TYR 0.008 0.001 TYR A 696 ARG 0.003 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.22 seconds wall clock time: 32 minutes 40.49 seconds (1960.49 seconds total)