Starting phenix.real_space_refine on Tue Mar 11 14:28:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd3_30643/03_2025/7dd3_30643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd3_30643/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dd3_30643/03_2025/7dd3_30643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd3_30643/03_2025/7dd3_30643.map" model { file = "/net/cci-nas-00/data/ceres_data/7dd3_30643/03_2025/7dd3_30643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd3_30643/03_2025/7dd3_30643.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.20, per 1000 atoms: 0.54 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: 1.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.16 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: 1.77 Time building geometry restraints manager: 1.48 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- 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= 0.769 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 (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: -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 TRP 0.026 0.004 TRP x 568 HIS 0.009 0.002 HIS y 142 PHE 0.039 0.004 PHE x 783 TYR 0.033 0.004 TYR x 795 ARG 0.013 0.002 ARG x 844 *********************** 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 : 0.695 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: 0.2229 time to fit residues: 48.1203 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 : 0.711 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.162591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115436 restraints weight = 7359.781| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.93 r_work: 0.3285 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6046 Z= 0.289 Angle : 0.668 9.381 8195 Z= 0.348 Chirality : 0.047 0.220 961 Planarity : 0.006 0.041 1008 Dihedral : 11.018 72.220 919 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.50 % Favored : 96.36 % Rotamer: Outliers : 3.85 % Allowed : 7.70 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.29), residues: 714 helix: -1.67 (0.25), residues: 306 sheet: -0.47 (0.54), residues: 96 loop : -1.48 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP x 568 HIS 0.007 0.001 HIS x 429 PHE 0.014 0.002 PHE x 863 TYR 0.029 0.002 TYR x 304 ARG 0.004 0.001 ARG x 289 *********************** 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 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8979 (mm) cc_final: 0.8406 (mm) REVERT: x 265 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7213 (t80) REVERT: x 309 GLU cc_start: 0.6975 (mp0) cc_final: 0.6536 (tp30) REVERT: x 346 ASP cc_start: 0.8582 (t0) cc_final: 0.8211 (t0) REVERT: x 373 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7685 (mptt) REVERT: x 488 GLN cc_start: 0.8541 (mt0) cc_final: 0.7821 (pp30) REVERT: x 725 GLN cc_start: 0.8696 (mt0) cc_final: 0.8389 (mt0) REVERT: x 796 GLN cc_start: 0.8250 (mt0) cc_final: 0.7538 (pt0) REVERT: x 851 LYS cc_start: 0.8293 (mmtm) cc_final: 0.7740 (mttm) REVERT: y 109 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8192 (tm) outliers start: 25 outliers final: 11 residues processed: 127 average time/residue: 0.1767 time to fit residues: 29.5512 Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 534 THR 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 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115333 restraints weight = 7304.250| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.92 r_work: 0.3274 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6046 Z= 0.261 Angle : 0.609 10.003 8195 Z= 0.311 Chirality : 0.045 0.207 961 Planarity : 0.005 0.038 1008 Dihedral : 10.124 60.236 911 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.70 % Allowed : 10.32 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.35 (0.31), residues: 714 helix: -0.75 (0.28), residues: 308 sheet: -0.24 (0.55), residues: 96 loop : -1.11 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.004 0.001 HIS x 429 PHE 0.015 0.002 PHE x 562 TYR 0.033 0.002 TYR x 304 ARG 0.005 0.000 ARG x 289 *********************** 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 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7893 (ttm) cc_final: 0.6820 (mmt) REVERT: x 255 GLN cc_start: 0.8295 (mp10) cc_final: 0.8034 (mp10) REVERT: x 265 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7252 (t80) REVERT: x 309 GLU cc_start: 0.6994 (mp0) cc_final: 0.6544 (tp30) REVERT: x 346 ASP cc_start: 0.8698 (t0) cc_final: 0.8210 (t0) REVERT: x 373 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7621 (mptt) REVERT: x 402 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.8007 (mmm-85) REVERT: x 488 GLN cc_start: 0.8486 (mt0) cc_final: 0.7866 (pp30) REVERT: x 690 ARG cc_start: 0.8402 (tmm-80) cc_final: 0.8196 (tmm-80) REVERT: x 796 GLN cc_start: 0.8244 (mt0) cc_final: 0.7523 (pt0) REVERT: x 851 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7713 (mttm) REVERT: y 96 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: y 109 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8164 (tm) outliers start: 24 outliers final: 10 residues processed: 113 average time/residue: 0.1808 time to fit residues: 27.1540 Evaluate side-chains 103 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 481 GLU Chi-restraints excluded: chain x residue 534 THR 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 96 GLU 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 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 50.0000 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 725 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.166673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119260 restraints weight = 7349.334| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.94 r_work: 0.3333 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3379 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= 0.148 Angle : 0.543 10.818 8195 Z= 0.274 Chirality : 0.043 0.180 961 Planarity : 0.004 0.034 1008 Dihedral : 9.777 62.224 908 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 2.47 % Allowed : 12.79 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.86 (0.31), residues: 714 helix: -0.18 (0.29), residues: 309 sheet: -0.20 (0.55), residues: 98 loop : -0.97 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.004 0.001 HIS x 429 PHE 0.020 0.001 PHE x 565 TYR 0.013 0.001 TYR x 515 ARG 0.005 0.000 ARG x 289 *********************** 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 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7943 (ttm) cc_final: 0.7287 (mmt) REVERT: x 265 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7355 (t80) REVERT: x 304 TYR cc_start: 0.7699 (p90) cc_final: 0.7400 (p90) REVERT: x 326 MET cc_start: 0.8361 (mtp) cc_final: 0.7942 (mtp) REVERT: x 346 ASP cc_start: 0.8624 (t0) cc_final: 0.8406 (t0) REVERT: x 373 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7580 (mptt) REVERT: x 380 THR cc_start: 0.9022 (p) cc_final: 0.8598 (p) REVERT: x 381 MET cc_start: 0.8332 (tpp) cc_final: 0.7706 (tpp) REVERT: x 488 GLN cc_start: 0.8480 (mt0) cc_final: 0.8006 (pp30) REVERT: x 680 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8503 (mm-30) REVERT: x 720 SER cc_start: 0.8980 (t) cc_final: 0.8664 (p) REVERT: x 796 GLN cc_start: 0.8227 (mt0) cc_final: 0.7459 (pt0) REVERT: x 851 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7734 (mttm) outliers start: 16 outliers final: 5 residues processed: 118 average time/residue: 0.1900 time to fit residues: 29.1550 Evaluate side-chains 99 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 481 GLU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain x residue 681 THR Chi-restraints excluded: chain x residue 836 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 258 GLN x 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118486 restraints weight = 7369.969| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.92 r_work: 0.3318 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3482 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= 0.176 Angle : 0.536 9.783 8195 Z= 0.272 Chirality : 0.043 0.157 961 Planarity : 0.004 0.033 1008 Dihedral : 9.534 63.929 904 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 2.62 % Allowed : 13.87 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.32), residues: 714 helix: 0.07 (0.30), residues: 306 sheet: -0.16 (0.56), residues: 98 loop : -0.87 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 PHE 0.014 0.001 PHE x 565 TYR 0.010 0.001 TYR x 515 ARG 0.007 0.000 ARG x 289 *********************** 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 111 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7871 (ttm) cc_final: 0.7268 (mmt) REVERT: x 265 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7324 (t80) REVERT: x 304 TYR cc_start: 0.7732 (p90) cc_final: 0.7364 (p90) REVERT: x 326 MET cc_start: 0.8348 (mtp) cc_final: 0.7871 (mtp) REVERT: x 346 ASP cc_start: 0.8653 (t0) cc_final: 0.8346 (t0) REVERT: x 373 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7643 (mptt) REVERT: x 380 THR cc_start: 0.9020 (p) cc_final: 0.8608 (p) REVERT: x 381 MET cc_start: 0.8405 (tpp) cc_final: 0.7855 (tpp) REVERT: x 577 MET cc_start: 0.8119 (mmm) cc_final: 0.7793 (mmm) REVERT: x 680 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8530 (mm-30) REVERT: x 720 SER cc_start: 0.8963 (t) cc_final: 0.8640 (p) REVERT: x 721 ARG cc_start: 0.9127 (ttt90) cc_final: 0.8543 (tpt-90) REVERT: x 725 GLN cc_start: 0.8913 (mt0) cc_final: 0.8369 (mp10) REVERT: x 796 GLN cc_start: 0.8231 (mt0) cc_final: 0.7499 (pt0) REVERT: x 851 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7969 (mmmm) REVERT: y 90 GLU cc_start: 0.7553 (tp30) cc_final: 0.7120 (tp30) REVERT: y 96 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7383 (mt-10) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1678 time to fit residues: 24.4993 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 : 0.601 ------------------------------------------------------------------------------- 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 319 LEU Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 481 GLU 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 x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116692 restraints weight = 7349.708| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.91 r_work: 0.3296 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6046 Z= 0.227 Angle : 0.554 8.443 8195 Z= 0.280 Chirality : 0.044 0.172 961 Planarity : 0.004 0.031 1008 Dihedral : 9.476 61.749 904 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.47 % Allowed : 14.18 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.41 (0.32), residues: 714 helix: 0.30 (0.30), residues: 307 sheet: -0.05 (0.56), residues: 96 loop : -0.82 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 PHE 0.020 0.001 PHE x 565 TYR 0.010 0.001 TYR x 475 ARG 0.008 0.000 ARG x 289 *********************** 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 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.642 Fit side-chains REVERT: x 245 MET cc_start: 0.7823 (ttm) cc_final: 0.7204 (mmt) REVERT: x 265 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7385 (t80) REVERT: x 304 TYR cc_start: 0.7696 (p90) cc_final: 0.7315 (p90) REVERT: x 309 GLU cc_start: 0.7223 (mp0) cc_final: 0.6291 (tp30) REVERT: x 326 MET cc_start: 0.8386 (mtp) cc_final: 0.7855 (mtp) REVERT: x 346 ASP cc_start: 0.8715 (t0) cc_final: 0.8514 (t0) REVERT: x 373 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7680 (mptt) REVERT: x 380 THR cc_start: 0.9012 (p) cc_final: 0.8571 (p) REVERT: x 381 MET cc_start: 0.8467 (tpp) cc_final: 0.7929 (tpp) REVERT: x 577 MET cc_start: 0.8130 (mmm) cc_final: 0.7763 (mmm) REVERT: x 680 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8569 (mm-30) REVERT: x 720 SER cc_start: 0.8994 (t) cc_final: 0.8659 (p) REVERT: x 796 GLN cc_start: 0.8268 (mt0) cc_final: 0.7553 (pt0) REVERT: x 851 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7969 (mmmm) REVERT: y 90 GLU cc_start: 0.7544 (tp30) cc_final: 0.7160 (tp30) REVERT: y 96 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7293 (mt-10) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.1563 time to fit residues: 22.0051 Evaluate side-chains 98 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 481 GLU 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 x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.165320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118171 restraints weight = 7309.284| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.90 r_work: 0.3314 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3663 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= 0.180 Angle : 0.535 7.949 8195 Z= 0.270 Chirality : 0.043 0.169 961 Planarity : 0.004 0.031 1008 Dihedral : 9.427 62.887 904 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 2.77 % Allowed : 14.02 % 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 (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: -0.34 (0.32), residues: 714 helix: 0.39 (0.30), residues: 308 sheet: -0.22 (0.55), residues: 98 loop : -0.75 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 714 HIS 0.003 0.001 HIS x 429 PHE 0.020 0.001 PHE x 565 TYR 0.010 0.001 TYR x 403 ARG 0.008 0.000 ARG x 289 *********************** 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 109 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.663 Fit side-chains REVERT: x 245 MET cc_start: 0.7789 (ttm) cc_final: 0.7329 (mmt) REVERT: x 265 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7438 (t80) REVERT: x 304 TYR cc_start: 0.7664 (p90) cc_final: 0.7270 (p90) REVERT: x 326 MET cc_start: 0.8376 (mtp) cc_final: 0.7821 (mtp) REVERT: x 346 ASP cc_start: 0.8712 (t0) cc_final: 0.8511 (t0) REVERT: x 373 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7759 (mptt) REVERT: x 380 THR cc_start: 0.9009 (p) cc_final: 0.8562 (p) REVERT: x 381 MET cc_start: 0.8471 (tpp) cc_final: 0.8045 (tpp) REVERT: x 577 MET cc_start: 0.8158 (mmm) cc_final: 0.7786 (mmm) REVERT: x 680 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8577 (mm-30) REVERT: x 720 SER cc_start: 0.9023 (t) cc_final: 0.8684 (p) REVERT: x 796 GLN cc_start: 0.8248 (mt0) cc_final: 0.7552 (pt0) REVERT: x 851 LYS cc_start: 0.8295 (mmtm) cc_final: 0.8016 (mmmm) REVERT: y 90 GLU cc_start: 0.7573 (tp30) cc_final: 0.7232 (tp30) outliers start: 18 outliers final: 13 residues processed: 106 average time/residue: 0.1608 time to fit residues: 23.6584 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 : 0.623 ------------------------------------------------------------------------------- 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 319 LEU 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 481 GLU 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 x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.161420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115781 restraints weight = 7432.408| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.80 r_work: 0.3308 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6046 Z= 0.162 Angle : 0.533 7.956 8195 Z= 0.270 Chirality : 0.043 0.163 961 Planarity : 0.004 0.031 1008 Dihedral : 9.403 64.432 904 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 2.77 % Allowed : 14.95 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.20 (0.32), residues: 714 helix: 0.51 (0.30), residues: 308 sheet: -0.38 (0.54), residues: 108 loop : -0.59 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 PHE 0.011 0.001 PHE x 565 TYR 0.011 0.001 TYR x 259 ARG 0.004 0.000 ARG x 289 *********************** 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 111 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.605 Fit side-chains REVERT: x 227 GLN cc_start: 0.8662 (mp10) cc_final: 0.8106 (tm-30) REVERT: x 245 MET cc_start: 0.7748 (ttm) cc_final: 0.7348 (mmt) REVERT: x 265 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.7419 (t80) REVERT: x 289 ARG cc_start: 0.7329 (mtm-85) cc_final: 0.7041 (mtm-85) REVERT: x 304 TYR cc_start: 0.7772 (p90) cc_final: 0.7315 (p90) REVERT: x 326 MET cc_start: 0.8310 (mtp) cc_final: 0.7766 (mtp) REVERT: x 373 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7859 (mptt) REVERT: x 380 THR cc_start: 0.8987 (p) cc_final: 0.8566 (p) REVERT: x 381 MET cc_start: 0.8494 (tpp) cc_final: 0.8109 (tpp) REVERT: x 528 VAL cc_start: 0.8141 (t) cc_final: 0.7890 (m) REVERT: x 577 MET cc_start: 0.8201 (mmm) cc_final: 0.7860 (mmm) REVERT: x 720 SER cc_start: 0.9007 (t) cc_final: 0.8723 (p) REVERT: x 796 GLN cc_start: 0.8294 (mt0) cc_final: 0.7592 (pt0) REVERT: x 851 LYS cc_start: 0.8252 (mmtm) cc_final: 0.8045 (mmmm) REVERT: x 858 MET cc_start: 0.8981 (mmm) cc_final: 0.8505 (tpt) REVERT: y 90 GLU cc_start: 0.7542 (tp30) cc_final: 0.7199 (tp30) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.1523 time to fit residues: 22.4861 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 : 0.600 ------------------------------------------------------------------------------- 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 371 THR Chi-restraints excluded: chain x residue 373 LYS Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 481 GLU 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 x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115528 restraints weight = 7659.283| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.94 r_work: 0.3314 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6046 Z= 0.158 Angle : 0.531 7.892 8195 Z= 0.268 Chirality : 0.043 0.166 961 Planarity : 0.004 0.030 1008 Dihedral : 9.358 66.228 904 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 2.31 % Allowed : 14.95 % 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 (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: -0.07 (0.32), residues: 714 helix: 0.66 (0.30), residues: 307 sheet: -0.27 (0.54), residues: 108 loop : -0.58 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 PHE 0.009 0.001 PHE x 562 TYR 0.011 0.001 TYR x 403 ARG 0.003 0.000 ARG x 289 *********************** 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 112 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.677 Fit side-chains REVERT: x 245 MET cc_start: 0.7705 (ttm) cc_final: 0.7345 (mmt) REVERT: x 255 GLN cc_start: 0.8356 (mp10) cc_final: 0.8065 (mp10) REVERT: x 265 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7377 (t80) REVERT: x 304 TYR cc_start: 0.7761 (p90) cc_final: 0.7304 (p90) REVERT: x 326 MET cc_start: 0.8305 (mtp) cc_final: 0.7711 (mtp) REVERT: x 346 ASP cc_start: 0.8482 (t0) cc_final: 0.7855 (t0) REVERT: x 373 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7905 (mptt) REVERT: x 380 THR cc_start: 0.8973 (p) cc_final: 0.8550 (p) REVERT: x 381 MET cc_start: 0.8500 (tpp) cc_final: 0.8221 (tpp) REVERT: x 528 VAL cc_start: 0.8108 (t) cc_final: 0.7879 (m) REVERT: x 577 MET cc_start: 0.8222 (mmm) cc_final: 0.7920 (mmm) REVERT: x 720 SER cc_start: 0.9001 (t) cc_final: 0.8720 (p) REVERT: x 796 GLN cc_start: 0.8296 (mt0) cc_final: 0.7594 (pt0) REVERT: y 90 GLU cc_start: 0.7538 (tp30) cc_final: 0.7191 (tp30) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.1700 time to fit residues: 24.6695 Evaluate side-chains 102 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 462 LEU Chi-restraints excluded: chain x residue 481 GLU 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 748 SER Chi-restraints excluded: chain x residue 836 MET Chi-restraints excluded: chain y residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.0270 chunk 10 optimal weight: 0.0970 chunk 38 optimal weight: 0.0040 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119187 restraints weight = 7461.690| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.82 r_work: 0.3362 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 6046 Z= 0.137 Angle : 0.541 8.074 8195 Z= 0.273 Chirality : 0.042 0.184 961 Planarity : 0.004 0.030 1008 Dihedral : 9.348 68.787 904 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 1.54 % Allowed : 16.49 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.01 (0.32), residues: 714 helix: 0.68 (0.30), residues: 309 sheet: -0.21 (0.54), residues: 111 loop : -0.53 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 PHE 0.011 0.001 PHE x 565 TYR 0.010 0.001 TYR x 403 ARG 0.003 0.000 ARG x 289 ********************** 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: 10 poor density : 95 time to evaluate : 0.626 Fit side-chains REVERT: x 227 GLN cc_start: 0.8693 (mp10) cc_final: 0.8484 (pt0) REVERT: x 255 GLN cc_start: 0.8362 (mp10) cc_final: 0.8070 (mp10) REVERT: x 265 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7476 (t80) REVERT: x 304 TYR cc_start: 0.7683 (p90) cc_final: 0.7250 (p90) REVERT: x 326 MET cc_start: 0.8197 (mtp) cc_final: 0.7586 (mtp) REVERT: x 346 ASP cc_start: 0.8379 (t0) cc_final: 0.8126 (t0) REVERT: x 381 MET cc_start: 0.8470 (tpp) cc_final: 0.8083 (tpp) REVERT: x 397 ASN cc_start: 0.9086 (t0) cc_final: 0.8646 (t0) REVERT: x 577 MET cc_start: 0.8128 (mmm) cc_final: 0.7843 (mmm) REVERT: x 720 SER cc_start: 0.9011 (t) cc_final: 0.8758 (p) REVERT: x 796 GLN cc_start: 0.8251 (mt0) cc_final: 0.7497 (pt0) REVERT: y 92 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.7703 (t) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.1582 time to fit residues: 21.9580 Evaluate side-chains 94 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE Chi-restraints excluded: chain x residue 462 LEU Chi-restraints excluded: chain x residue 513 ILE Chi-restraints excluded: chain x residue 571 LEU Chi-restraints excluded: chain x residue 616 LEU Chi-restraints excluded: chain y residue 92 VAL 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 39 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116308 restraints weight = 7595.805| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.82 r_work: 0.3320 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6046 Z= 0.186 Angle : 0.568 7.508 8195 Z= 0.289 Chirality : 0.043 0.164 961 Planarity : 0.004 0.030 1008 Dihedral : 9.334 67.245 904 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.64 % Favored : 96.22 % Rotamer: Outliers : 1.23 % Allowed : 17.10 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.04 (0.32), residues: 714 helix: 0.72 (0.30), residues: 308 sheet: -0.21 (0.54), residues: 111 loop : -0.50 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS x 226 PHE 0.009 0.001 PHE x 863 TYR 0.011 0.001 TYR x 403 ARG 0.004 0.000 ARG x 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.72 seconds wall clock time: 62 minutes 53.69 seconds (3773.69 seconds total)