Starting phenix.real_space_refine on Fri Aug 22 16:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd3_30643/08_2025/7dd3_30643.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 34 5.16 5 C 3756 2.51 5 N 1000 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5929 Number of models: 1 Model: "" Number of chains: 3 Chain: "x" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5193 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 164 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 5} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.05, per 1000 atoms: 0.18 Number of scatterers: 5929 At special positions: 0 Unit cell: (145.22, 115.54, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 9 15.00 O 1130 8.00 N 1000 7.00 C 3756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 207.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 47.0% alpha, 11.0% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'x' and resid 215 through 221 removed outlier: 3.988A pdb=" N LYS x 221 " --> pdb=" O GLN x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 223 through 227 removed outlier: 3.533A pdb=" N GLN x 227 " --> pdb=" O PRO x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 228 through 239 removed outlier: 4.254A pdb=" N GLN x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 254 through 264 removed outlier: 4.218A pdb=" N GLN x 258 " --> pdb=" O THR x 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU x 260 " --> pdb=" O LEU x 256 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL x 261 " --> pdb=" O PRO x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 279 through 294 removed outlier: 3.552A pdb=" N THR x 284 " --> pdb=" O ARG x 280 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG x 289 " --> pdb=" O SER x 285 " (cutoff:3.500A) Processing helix chain 'x' and resid 323 through 334 removed outlier: 3.654A pdb=" N LEU x 327 " --> pdb=" O THR x 323 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG x 329 " --> pdb=" O GLY x 325 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE x 331 " --> pdb=" O LEU x 327 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU x 332 " --> pdb=" O LEU x 328 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 352 through 369 removed outlier: 4.135A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU x 366 " --> pdb=" O LEU x 362 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.799A pdb=" N PHE x 386 " --> pdb=" O ASN x 382 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER x 387 " --> pdb=" O ALA x 383 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU x 388 " --> pdb=" O LYS x 384 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE x 389 " --> pdb=" O LYS x 385 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 432 removed outlier: 3.534A pdb=" N ALA x 420 " --> pdb=" O ASN x 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE x 426 " --> pdb=" O ILE x 422 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 445 through 462 removed outlier: 3.806A pdb=" N THR x 451 " --> pdb=" O GLU x 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE x 458 " --> pdb=" O LYS x 454 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER x 460 " --> pdb=" O GLU x 456 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 484 Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 573 Processing helix chain 'x' and resid 580 through 585 removed outlier: 3.565A pdb=" N ARG x 584 " --> pdb=" O PRO x 580 " (cutoff:3.500A) Processing helix chain 'x' and resid 589 through 597 Processing helix chain 'x' and resid 612 through 626 removed outlier: 3.654A pdb=" N SER x 619 " --> pdb=" O THR x 615 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU x 620 " --> pdb=" O LEU x 616 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU x 626 " --> pdb=" O ASN x 622 " (cutoff:3.500A) Processing helix chain 'x' and resid 636 through 645 removed outlier: 3.694A pdb=" N MET x 641 " --> pdb=" O ARG x 637 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS x 643 " --> pdb=" O GLY x 639 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU x 644 " --> pdb=" O LYS x 640 " (cutoff:3.500A) Processing helix chain 'x' and resid 650 through 658 removed outlier: 3.604A pdb=" N VAL x 654 " --> pdb=" O GLU x 650 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR x 656 " --> pdb=" O ALA x 652 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 679 removed outlier: 4.164A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.725A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL x 696 " --> pdb=" O ALA x 692 " (cutoff:3.500A) Processing helix chain 'x' and resid 704 through 716 Processing helix chain 'x' and resid 721 through 727 removed outlier: 3.710A pdb=" N GLN x 725 " --> pdb=" O ARG x 721 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 751 Processing helix chain 'x' and resid 752 through 763 removed outlier: 3.782A pdb=" N LYS x 756 " --> pdb=" O GLY x 752 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN x 759 " --> pdb=" O GLU x 755 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA x 760 " --> pdb=" O LYS x 756 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG x 761 " --> pdb=" O ASN x 757 " (cutoff:3.500A) Processing helix chain 'x' and resid 770 through 783 removed outlier: 3.889A pdb=" N THR x 776 " --> pdb=" O ASN x 772 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG x 777 " --> pdb=" O ALA x 773 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER x 781 " --> pdb=" O ARG x 777 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.563A pdb=" N HIS x 819 " --> pdb=" O LEU x 815 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 859 removed outlier: 4.129A pdb=" N ILE x 856 " --> pdb=" O GLU x 852 " (cutoff:3.500A) Processing helix chain 'x' and resid 859 through 867 removed outlier: 6.378A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE x 867 " --> pdb=" O PHE x 863 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 14 Processing helix chain 'y' and resid 93 through 100 removed outlier: 3.865A pdb=" N TYR y 97 " --> pdb=" O THR y 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN y 98 " --> pdb=" O GLU y 94 " (cutoff:3.500A) Processing helix chain 'y' and resid 101 through 112 removed outlier: 4.142A pdb=" N GLY y 106 " --> pdb=" O VAL y 102 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP y 107 " --> pdb=" O GLU y 103 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU y 110 " --> pdb=" O GLY y 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 7.443A pdb=" N GLN x 272 " --> pdb=" O CYS x 342 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N MET x 344 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA x 274 " --> pdb=" O MET x 344 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER x 341 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU x 375 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE x 343 " --> pdb=" O LEU x 375 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER x 377 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE x 345 " --> pdb=" O SER x 377 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE x 396 " --> pdb=" O VAL x 241 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE x 243 " --> pdb=" O PHE x 396 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL x 398 " --> pdb=" O ILE x 243 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N MET x 245 " --> pdb=" O VAL x 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 406 through 409 removed outlier: 6.267A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 528 Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 3.690A pdb=" N VAL x 830 " --> pdb=" O VAL x 788 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809 removed outlier: 6.803A pdb=" N SER x 808 " --> pdb=" O ILE x 843 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 190 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1616 1.33 - 1.45: 928 1.45 - 1.57: 3429 1.57 - 1.69: 18 1.69 - 1.80: 55 Bond restraints: 6046 Sorted by residual: bond pdb=" N THR y 93 " pdb=" CA THR y 93 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 bond pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.48e+00 bond pdb=" CG LEU x 835 " pdb=" CD1 LEU x 835 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.60e+00 bond pdb=" CB VAL x 788 " pdb=" CG2 VAL x 788 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.48e+00 bond pdb=" CG LEU x 831 " pdb=" CD2 LEU x 831 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.18e+00 ... (remaining 6041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 7686 2.02 - 4.03: 427 4.03 - 6.05: 64 6.05 - 8.07: 12 8.07 - 10.09: 6 Bond angle restraints: 8195 Sorted by residual: angle pdb=" C LYS x 300 " pdb=" N GLU x 301 " pdb=" CA GLU x 301 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" N THR x 681 " pdb=" CA THR x 681 " pdb=" C THR x 681 " ideal model delta sigma weight residual 109.81 118.85 -9.04 2.21e+00 2.05e-01 1.67e+01 angle pdb=" N ILE x 273 " pdb=" CA ILE x 273 " pdb=" C ILE x 273 " ideal model delta sigma weight residual 109.21 114.59 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" CB MET x 322 " pdb=" CG MET x 322 " pdb=" SD MET x 322 " ideal model delta sigma weight residual 112.70 102.61 10.09 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta sigma weight residual 110.49 116.11 -5.62 1.69e+00 3.50e-01 1.11e+01 ... (remaining 8190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 3492 16.59 - 33.19: 166 33.19 - 49.78: 62 49.78 - 66.37: 21 66.37 - 82.96: 3 Dihedral angle restraints: 3744 sinusoidal: 1635 harmonic: 2109 Sorted by residual: dihedral pdb=" C THR y 93 " pdb=" N THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta harmonic sigma weight residual -122.00 -134.68 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N THR y 93 " pdb=" C THR y 93 " pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta harmonic sigma weight residual 123.40 135.17 -11.77 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA ARG x 584 " pdb=" C ARG x 584 " pdb=" N THR x 585 " pdb=" CA THR x 585 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 742 0.074 - 0.148: 200 0.148 - 0.222: 16 0.222 - 0.296: 1 0.296 - 0.370: 2 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA THR y 93 " pdb=" N THR y 93 " pdb=" C THR y 93 " pdb=" CB THR y 93 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB ILE x 843 " pdb=" CA ILE x 843 " pdb=" CG1 ILE x 843 " pdb=" CG2 ILE x 843 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA THR x 681 " pdb=" N THR x 681 " pdb=" C THR x 681 " pdb=" CB THR x 681 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 958 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE x 783 " -0.008 2.00e-02 2.50e+03 2.02e-02 7.17e+00 pdb=" CG PHE x 783 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE x 783 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE x 783 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE x 783 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE x 783 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE x 783 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU x 223 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO x 224 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO x 224 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO x 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS x 810 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO x 811 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO x 811 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO x 811 " -0.030 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1995 2.87 - 3.37: 5326 3.37 - 3.88: 9135 3.88 - 4.39: 10580 4.39 - 4.90: 17919 Nonbonded interactions: 44955 Sorted by model distance: nonbonded pdb=" OE1 GLN x 305 " pdb=" NZ LYS x 320 " model vdw 2.357 3.120 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.362 3.120 nonbonded pdb=" O LEU x 508 " pdb=" NH2 ARG x 552 " model vdw 2.363 3.120 nonbonded pdb=" O ALA x 420 " pdb=" OG1 THR x 424 " model vdw 2.399 3.040 nonbonded pdb=" NZ LYS x 363 " pdb=" O PHE x 389 " model vdw 2.411 3.120 ... (remaining 44950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.012 0.080 6046 Z= 0.476 Angle : 1.056 10.087 8195 Z= 0.562 Chirality : 0.064 0.370 961 Planarity : 0.008 0.055 1008 Dihedral : 12.444 82.961 2376 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.32 % Favored : 94.54 % Rotamer: Outliers : 2.31 % Allowed : 4.01 % Favored : 93.68 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.77 (0.26), residues: 714 helix: -3.83 (0.15), residues: 269 sheet: -1.38 (0.46), residues: 122 loop : -1.52 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG x 844 TYR 0.033 0.004 TYR x 795 PHE 0.039 0.004 PHE x 783 TRP 0.026 0.004 TRP x 568 HIS 0.009 0.002 HIS y 142 Details of bonding type rmsd covalent geometry : bond 0.01167 ( 6046) covalent geometry : angle 1.05634 ( 8195) hydrogen bonds : bond 0.32991 ( 190) hydrogen bonds : angle 9.21972 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8840 (mm) cc_final: 0.8451 (mm) REVERT: x 272 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: x 488 GLN cc_start: 0.8230 (mt0) cc_final: 0.7638 (pp30) REVERT: x 758 ASP cc_start: 0.7587 (m-30) cc_final: 0.7277 (m-30) REVERT: x 796 GLN cc_start: 0.8134 (mt0) cc_final: 0.7810 (pt0) REVERT: y 109 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (tm) outliers start: 15 outliers final: 4 residues processed: 173 average time/residue: 0.0736 time to fit residues: 16.0952 Evaluate side-chains 100 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 268 GLN Chi-restraints excluded: chain x residue 271 LEU Chi-restraints excluded: chain x residue 272 GLN Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 90 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 239 ASN x 382 ASN x 412 GLN x 419 HIS x 427 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118319 restraints weight = 7343.678| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.96 r_work: 0.3321 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6046 Z= 0.135 Angle : 0.639 9.420 8195 Z= 0.332 Chirality : 0.045 0.238 961 Planarity : 0.005 0.042 1008 Dihedral : 10.871 67.721 919 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.24 % Allowed : 8.63 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.28), residues: 714 helix: -1.66 (0.25), residues: 306 sheet: -0.30 (0.54), residues: 96 loop : -1.47 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG x 289 TYR 0.031 0.002 TYR x 304 PHE 0.012 0.001 PHE x 863 TRP 0.011 0.001 TRP x 568 HIS 0.007 0.001 HIS x 429 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 6046) covalent geometry : angle 0.63916 ( 8195) hydrogen bonds : bond 0.04374 ( 190) hydrogen bonds : angle 4.97319 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8980 (mm) cc_final: 0.8418 (mm) REVERT: x 265 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7312 (t80) REVERT: x 304 TYR cc_start: 0.7659 (p90) cc_final: 0.7404 (p90) REVERT: x 309 GLU cc_start: 0.6886 (mp0) cc_final: 0.6459 (tp30) REVERT: x 346 ASP cc_start: 0.8503 (t0) cc_final: 0.8074 (t0) REVERT: x 373 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7706 (mptt) REVERT: x 488 GLN cc_start: 0.8504 (mt0) cc_final: 0.7830 (pp30) REVERT: x 721 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8456 (ttt90) REVERT: x 725 GLN cc_start: 0.8677 (mt0) cc_final: 0.7941 (mt0) REVERT: x 758 ASP cc_start: 0.8150 (m-30) cc_final: 0.7839 (m-30) REVERT: x 796 GLN cc_start: 0.8159 (mt0) cc_final: 0.7363 (pt0) REVERT: y 90 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: y 109 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8176 (tm) outliers start: 21 outliers final: 8 residues processed: 127 average time/residue: 0.0528 time to fit residues: 9.0063 Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 332 LEU Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 90 GLU Chi-restraints excluded: chain y residue 93 THR Chi-restraints excluded: chain y residue 96 GLU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 258 GLN x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120192 restraints weight = 7255.008| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.94 r_work: 0.3325 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6046 Z= 0.109 Angle : 0.568 9.702 8195 Z= 0.287 Chirality : 0.043 0.179 961 Planarity : 0.004 0.036 1008 Dihedral : 10.142 64.466 911 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.62 % Allowed : 10.94 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.31), residues: 714 helix: -0.63 (0.28), residues: 304 sheet: -0.02 (0.56), residues: 98 loop : -1.07 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 289 TYR 0.028 0.002 TYR x 304 PHE 0.019 0.001 PHE x 565 TRP 0.005 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6046) covalent geometry : angle 0.56849 ( 8195) hydrogen bonds : bond 0.03581 ( 190) hydrogen bonds : angle 4.35246 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7803 (ttm) cc_final: 0.7150 (mmt) REVERT: x 265 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7291 (t80) REVERT: x 304 TYR cc_start: 0.7819 (p90) cc_final: 0.7555 (p90) REVERT: x 309 GLU cc_start: 0.6847 (mp0) cc_final: 0.6486 (tp30) REVERT: x 346 ASP cc_start: 0.8566 (t0) cc_final: 0.8331 (t0) REVERT: x 373 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7580 (mptt) REVERT: x 381 MET cc_start: 0.8065 (ttm) cc_final: 0.7835 (tpp) REVERT: x 488 GLN cc_start: 0.8474 (mt0) cc_final: 0.7911 (pp30) REVERT: x 690 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8086 (tmm-80) REVERT: x 720 SER cc_start: 0.8969 (t) cc_final: 0.8713 (p) REVERT: x 725 GLN cc_start: 0.8727 (mt0) cc_final: 0.8369 (mp10) REVERT: x 758 ASP cc_start: 0.8079 (m-30) cc_final: 0.7659 (m-30) REVERT: x 762 MET cc_start: 0.7439 (mmp) cc_final: 0.7207 (mmp) REVERT: x 796 GLN cc_start: 0.8147 (mt0) cc_final: 0.7326 (pt0) REVERT: x 851 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7714 (mttm) REVERT: y 109 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8174 (tm) outliers start: 17 outliers final: 7 residues processed: 121 average time/residue: 0.0632 time to fit residues: 10.0169 Evaluate side-chains 109 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 332 LEU Chi-restraints excluded: chain x residue 338 SER Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain x residue 837 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.164653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116272 restraints weight = 7297.357| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.96 r_work: 0.3284 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6046 Z= 0.152 Angle : 0.563 8.067 8195 Z= 0.290 Chirality : 0.044 0.180 961 Planarity : 0.004 0.034 1008 Dihedral : 9.738 62.995 908 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.70 % Allowed : 12.17 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.31), residues: 714 helix: -0.22 (0.29), residues: 306 sheet: 0.02 (0.56), residues: 96 loop : -0.95 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 289 TYR 0.023 0.002 TYR x 304 PHE 0.017 0.001 PHE x 565 TRP 0.005 0.001 TRP x 714 HIS 0.002 0.001 HIS x 704 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6046) covalent geometry : angle 0.56319 ( 8195) hydrogen bonds : bond 0.03769 ( 190) hydrogen bonds : angle 4.20104 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.236 Fit side-chains REVERT: x 245 MET cc_start: 0.7841 (ttm) cc_final: 0.7157 (mmt) REVERT: x 265 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7371 (t80) REVERT: x 289 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: x 304 TYR cc_start: 0.7890 (p90) cc_final: 0.7653 (p90) REVERT: x 309 GLU cc_start: 0.6946 (mp0) cc_final: 0.6480 (tp30) REVERT: x 326 MET cc_start: 0.8479 (mtp) cc_final: 0.8002 (mtp) REVERT: x 339 LYS cc_start: 0.8695 (mttt) cc_final: 0.8460 (mtpt) REVERT: x 346 ASP cc_start: 0.8646 (t0) cc_final: 0.8419 (t0) REVERT: x 373 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7624 (mptt) REVERT: x 380 THR cc_start: 0.9032 (p) cc_final: 0.8645 (p) REVERT: x 381 MET cc_start: 0.8223 (ttm) cc_final: 0.7992 (tpp) REVERT: x 488 GLN cc_start: 0.8499 (mt0) cc_final: 0.7932 (pp30) REVERT: x 720 SER cc_start: 0.8942 (t) cc_final: 0.8661 (p) REVERT: x 721 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8553 (ttt90) REVERT: x 725 GLN cc_start: 0.8846 (mt0) cc_final: 0.8326 (mp10) REVERT: x 758 ASP cc_start: 0.8071 (m-30) cc_final: 0.7627 (m-30) REVERT: x 762 MET cc_start: 0.7489 (mmp) cc_final: 0.7263 (mmp) REVERT: x 796 GLN cc_start: 0.8229 (mt0) cc_final: 0.7525 (pt0) REVERT: x 851 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7717 (mmmm) REVERT: y 109 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8215 (tm) outliers start: 24 outliers final: 10 residues processed: 117 average time/residue: 0.0724 time to fit residues: 11.1460 Evaluate side-chains 107 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 256 LEU Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 721 ARG Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.167418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119421 restraints weight = 7465.914| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.99 r_work: 0.3341 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6046 Z= 0.095 Angle : 0.519 7.895 8195 Z= 0.265 Chirality : 0.042 0.162 961 Planarity : 0.004 0.033 1008 Dihedral : 9.575 65.649 906 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.77 % Allowed : 13.10 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.32), residues: 714 helix: 0.21 (0.30), residues: 307 sheet: -0.11 (0.55), residues: 98 loop : -0.78 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.019 0.001 TYR x 304 PHE 0.013 0.001 PHE x 565 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6046) covalent geometry : angle 0.51878 ( 8195) hydrogen bonds : bond 0.02959 ( 190) hydrogen bonds : angle 3.96344 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7837 (ttm) cc_final: 0.7267 (mmt) REVERT: x 265 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7418 (t80) REVERT: x 304 TYR cc_start: 0.7846 (p90) cc_final: 0.7296 (p90) REVERT: x 326 MET cc_start: 0.8394 (mtp) cc_final: 0.7833 (mtp) REVERT: x 339 LYS cc_start: 0.8641 (mttt) cc_final: 0.8398 (mtpt) REVERT: x 346 ASP cc_start: 0.8613 (t0) cc_final: 0.8359 (t0) REVERT: x 373 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7723 (mptt) REVERT: x 380 THR cc_start: 0.9004 (p) cc_final: 0.8639 (p) REVERT: x 720 SER cc_start: 0.8936 (t) cc_final: 0.8635 (p) REVERT: x 758 ASP cc_start: 0.8064 (m-30) cc_final: 0.7593 (m-30) REVERT: x 796 GLN cc_start: 0.8195 (mt0) cc_final: 0.7434 (pt0) REVERT: x 851 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7977 (mmmm) REVERT: y 109 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (tm) outliers start: 18 outliers final: 7 residues processed: 116 average time/residue: 0.0766 time to fit residues: 12.0118 Evaluate side-chains 101 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 368 GLN Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.117961 restraints weight = 7408.256| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.94 r_work: 0.3313 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6046 Z= 0.125 Angle : 0.530 7.405 8195 Z= 0.275 Chirality : 0.043 0.169 961 Planarity : 0.004 0.031 1008 Dihedral : 9.545 65.526 906 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 2.47 % Allowed : 14.33 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.32), residues: 714 helix: 0.34 (0.30), residues: 307 sheet: -0.05 (0.55), residues: 98 loop : -0.79 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 289 TYR 0.018 0.001 TYR x 304 PHE 0.009 0.001 PHE x 562 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS y 142 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6046) covalent geometry : angle 0.53030 ( 8195) hydrogen bonds : bond 0.03274 ( 190) hydrogen bonds : angle 3.99297 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.192 Fit side-chains REVERT: x 245 MET cc_start: 0.7842 (ttm) cc_final: 0.7260 (mmt) REVERT: x 265 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7494 (t80) REVERT: x 304 TYR cc_start: 0.7796 (p90) cc_final: 0.7485 (p90) REVERT: x 309 GLU cc_start: 0.7044 (mp0) cc_final: 0.6308 (tp30) REVERT: x 326 MET cc_start: 0.8364 (mtp) cc_final: 0.7813 (mtp) REVERT: x 373 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7752 (mptt) REVERT: x 380 THR cc_start: 0.9040 (p) cc_final: 0.8584 (p) REVERT: x 381 MET cc_start: 0.8349 (tpp) cc_final: 0.7754 (tpp) REVERT: x 720 SER cc_start: 0.8973 (t) cc_final: 0.8654 (p) REVERT: x 725 GLN cc_start: 0.8861 (mt0) cc_final: 0.8452 (mp10) REVERT: x 758 ASP cc_start: 0.8072 (m-30) cc_final: 0.7585 (m-30) REVERT: x 796 GLN cc_start: 0.8217 (mt0) cc_final: 0.7478 (pt0) REVERT: y 90 GLU cc_start: 0.7585 (tp30) cc_final: 0.7217 (tp30) REVERT: y 96 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7412 (mt-10) REVERT: y 109 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8211 (tm) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.0781 time to fit residues: 11.1540 Evaluate side-chains 102 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 319 LEU Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.0070 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.0170 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118672 restraints weight = 7383.469| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.95 r_work: 0.3322 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6046 Z= 0.113 Angle : 0.516 7.294 8195 Z= 0.267 Chirality : 0.042 0.168 961 Planarity : 0.004 0.032 1008 Dihedral : 9.491 65.719 906 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.93 % Allowed : 14.18 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.32), residues: 714 helix: 0.49 (0.30), residues: 308 sheet: 0.01 (0.55), residues: 98 loop : -0.74 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 289 TYR 0.016 0.001 TYR x 304 PHE 0.012 0.001 PHE x 565 TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6046) covalent geometry : angle 0.51580 ( 8195) hydrogen bonds : bond 0.03058 ( 190) hydrogen bonds : angle 3.93065 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7801 (ttm) cc_final: 0.7286 (mmt) REVERT: x 265 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7477 (t80) REVERT: x 304 TYR cc_start: 0.7738 (p90) cc_final: 0.7360 (p90) REVERT: x 326 MET cc_start: 0.8341 (mtp) cc_final: 0.7778 (mtp) REVERT: x 346 ASP cc_start: 0.8541 (t0) cc_final: 0.8229 (t0) REVERT: x 373 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7768 (mptt) REVERT: x 380 THR cc_start: 0.9001 (p) cc_final: 0.8585 (p) REVERT: x 381 MET cc_start: 0.8456 (tpp) cc_final: 0.7990 (tpp) REVERT: x 720 SER cc_start: 0.9000 (t) cc_final: 0.8662 (p) REVERT: x 725 GLN cc_start: 0.8836 (mt0) cc_final: 0.8414 (mp10) REVERT: x 758 ASP cc_start: 0.8041 (m-30) cc_final: 0.7561 (m-30) REVERT: x 796 GLN cc_start: 0.8216 (mt0) cc_final: 0.7475 (pt0) REVERT: y 90 GLU cc_start: 0.7631 (tp30) cc_final: 0.7278 (tp30) REVERT: y 109 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8189 (tm) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.0699 time to fit residues: 10.4355 Evaluate side-chains 102 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115489 restraints weight = 7585.505| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.87 r_work: 0.3312 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6046 Z= 0.107 Angle : 0.522 7.231 8195 Z= 0.268 Chirality : 0.042 0.168 961 Planarity : 0.004 0.032 1008 Dihedral : 9.459 66.933 906 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 2.62 % Allowed : 14.64 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.32), residues: 714 helix: 0.64 (0.30), residues: 308 sheet: 0.09 (0.55), residues: 98 loop : -0.71 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.015 0.001 TYR x 304 PHE 0.008 0.001 PHE x 863 TRP 0.005 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6046) covalent geometry : angle 0.52244 ( 8195) hydrogen bonds : bond 0.02974 ( 190) hydrogen bonds : angle 3.87637 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7772 (ttm) cc_final: 0.7480 (mmt) REVERT: x 265 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7452 (t80) REVERT: x 304 TYR cc_start: 0.7774 (p90) cc_final: 0.7408 (p90) REVERT: x 309 GLU cc_start: 0.7115 (mp0) cc_final: 0.6313 (tp30) REVERT: x 326 MET cc_start: 0.8310 (mtp) cc_final: 0.7685 (mtp) REVERT: x 346 ASP cc_start: 0.8464 (t0) cc_final: 0.8221 (t0) REVERT: x 381 MET cc_start: 0.8481 (tpp) cc_final: 0.8165 (tpp) REVERT: x 720 SER cc_start: 0.9031 (t) cc_final: 0.8721 (p) REVERT: x 721 ARG cc_start: 0.9133 (ttt90) cc_final: 0.8648 (tpt-90) REVERT: x 725 GLN cc_start: 0.8764 (mt0) cc_final: 0.8226 (mp10) REVERT: x 758 ASP cc_start: 0.8055 (m-30) cc_final: 0.7624 (m-30) REVERT: x 796 GLN cc_start: 0.8279 (mt0) cc_final: 0.7574 (pt0) REVERT: x 858 MET cc_start: 0.8976 (mmm) cc_final: 0.8494 (tpt) REVERT: y 90 GLU cc_start: 0.7596 (tp30) cc_final: 0.7324 (tp30) REVERT: y 109 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8251 (tm) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.0713 time to fit residues: 10.2019 Evaluate side-chains 101 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 469 MET Chi-restraints excluded: chain x residue 511 ASP Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.0470 chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.163365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117658 restraints weight = 7559.344| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.78 r_work: 0.3344 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6046 Z= 0.095 Angle : 0.512 7.274 8195 Z= 0.263 Chirality : 0.042 0.165 961 Planarity : 0.004 0.032 1008 Dihedral : 9.420 68.218 906 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.47 % Allowed : 15.41 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.32), residues: 714 helix: 0.72 (0.30), residues: 311 sheet: -0.04 (0.54), residues: 105 loop : -0.70 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.016 0.001 TYR x 304 PHE 0.011 0.001 PHE x 565 TRP 0.006 0.001 TRP x 568 HIS 0.002 0.000 HIS x 226 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6046) covalent geometry : angle 0.51207 ( 8195) hydrogen bonds : bond 0.02740 ( 190) hydrogen bonds : angle 3.81038 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7722 (ttm) cc_final: 0.7465 (mmt) REVERT: x 265 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7483 (t80) REVERT: x 304 TYR cc_start: 0.7717 (p90) cc_final: 0.7150 (p90) REVERT: x 326 MET cc_start: 0.8250 (mtp) cc_final: 0.7629 (mtp) REVERT: x 346 ASP cc_start: 0.8473 (t0) cc_final: 0.8213 (t0) REVERT: x 720 SER cc_start: 0.8989 (t) cc_final: 0.8707 (p) REVERT: x 721 ARG cc_start: 0.9144 (ttt90) cc_final: 0.8679 (tpt-90) REVERT: x 725 GLN cc_start: 0.8731 (mt0) cc_final: 0.8219 (mp10) REVERT: x 796 GLN cc_start: 0.8269 (mt0) cc_final: 0.7543 (pt0) REVERT: y 90 GLU cc_start: 0.7622 (tp30) cc_final: 0.7365 (tp30) REVERT: y 109 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8200 (tm) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.0678 time to fit residues: 9.8477 Evaluate side-chains 99 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 368 GLN Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114591 restraints weight = 7781.006| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.97 r_work: 0.3302 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6046 Z= 0.125 Angle : 0.542 7.360 8195 Z= 0.276 Chirality : 0.043 0.167 961 Planarity : 0.004 0.032 1008 Dihedral : 9.412 66.746 906 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 2.31 % Allowed : 16.18 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.32), residues: 714 helix: 0.72 (0.30), residues: 312 sheet: -0.22 (0.54), residues: 107 loop : -0.45 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.016 0.001 TYR x 304 PHE 0.008 0.001 PHE x 863 TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS y 142 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6046) covalent geometry : angle 0.54179 ( 8195) hydrogen bonds : bond 0.03110 ( 190) hydrogen bonds : angle 3.88827 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.141 Fit side-chains REVERT: x 245 MET cc_start: 0.7774 (ttm) cc_final: 0.7488 (mmt) REVERT: x 265 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.7494 (t80) REVERT: x 304 TYR cc_start: 0.7754 (p90) cc_final: 0.7396 (p90) REVERT: x 309 GLU cc_start: 0.7207 (mp0) cc_final: 0.6271 (tp30) REVERT: x 326 MET cc_start: 0.8323 (mtp) cc_final: 0.7720 (mtp) REVERT: x 346 ASP cc_start: 0.8489 (t0) cc_final: 0.8205 (t0) REVERT: x 373 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7920 (mptt) REVERT: x 720 SER cc_start: 0.9001 (t) cc_final: 0.8702 (p) REVERT: x 721 ARG cc_start: 0.9172 (ttt90) cc_final: 0.8719 (tpt-90) REVERT: x 725 GLN cc_start: 0.8731 (mt0) cc_final: 0.8243 (mp10) REVERT: x 796 GLN cc_start: 0.8309 (mt0) cc_final: 0.7627 (pt0) REVERT: x 851 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7962 (mmtp) REVERT: y 90 GLU cc_start: 0.7632 (tp30) cc_final: 0.7357 (tp30) REVERT: y 96 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7370 (mt-10) REVERT: y 109 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8246 (tm) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.0663 time to fit residues: 9.2537 Evaluate side-chains 100 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 352 THR Chi-restraints excluded: chain x residue 368 GLN Chi-restraints excluded: chain x residue 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain y residue 71 LEU Chi-restraints excluded: chain y residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 382 ASN ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.163672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115893 restraints weight = 7744.376| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.96 r_work: 0.3325 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6046 Z= 0.108 Angle : 0.531 7.254 8195 Z= 0.270 Chirality : 0.042 0.165 961 Planarity : 0.004 0.030 1008 Dihedral : 9.370 66.140 906 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.16 % Allowed : 16.80 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.32), residues: 714 helix: 0.80 (0.30), residues: 312 sheet: 0.04 (0.55), residues: 101 loop : -0.63 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 289 TYR 0.015 0.001 TYR x 304 PHE 0.022 0.001 PHE x 396 TRP 0.005 0.001 TRP x 714 HIS 0.002 0.001 HIS x 572 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6046) covalent geometry : angle 0.53068 ( 8195) hydrogen bonds : bond 0.02900 ( 190) hydrogen bonds : angle 3.79855 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.55 seconds wall clock time: 28 minutes 4.31 seconds (1684.31 seconds total)