Starting phenix.real_space_refine on Thu Jul 2 02:38:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_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_30643/07_2026/7dd3_30643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.map" model { file = "/net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dd3_30643/07_2026/7dd3_30643.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.40, per 1000 atoms: 0.24 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: 0.48 Conformation dependent library (CDL) restraints added in 209.1 milliseconds 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: 0.73 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: 0.72 Time building geometry restraints manager: 0.67 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: 3478 16.59 - 33.19: 161 33.19 - 49.78: 59 49.78 - 66.37: 11 66.37 - 82.96: 3 Dihedral angle restraints: 3712 sinusoidal: 1603 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 3709 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: 0.600 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 11.804 82.961 2344 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 are 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/Z covalent geometry : bond 0.01167 / 0.48 ( 6046) covalent geometry : angle 1.05634 / 0.56 ( 8195) hydrogen bonds : bond 0.32991 / 20.91 ( 190) hydrogen bonds : angle 9.21972 / 6.39 ( 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 : 0.181 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: 0.8135 (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: 0.0836 time to fit residues: 18.2922 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 : 0.199 ------------------------------------------------------------------------------- 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... 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 = 0.4051 r_free = 0.4051 target = 0.166332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118654 restraints weight = 7335.626| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.98 r_work: 0.3319 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6046 Z= 0.136 Angle : 0.636 9.412 8195 Z= 0.331 Chirality : 0.045 0.243 961 Planarity : 0.005 0.042 1008 Dihedral : 8.887 67.768 887 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.08 % Allowed : 8.78 % 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 are not related in a simple way. whole: -2.19 (0.29), residues: 714 helix: -1.65 (0.25), residues: 306 sheet: -0.29 (0.54), residues: 96 loop : -1.47 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 289 TYR 0.031 0.002 TYR x 304 PHE 0.011 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/Z covalent geometry : bond 0.00305 / 0.14 ( 6046) covalent geometry : angle 0.63644 / 0.33 ( 8195) hydrogen bonds : bond 0.04297 / 2.78 ( 190) hydrogen bonds : angle 4.97038 / 3.51 ( 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 134 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 256 LEU cc_start: 0.8972 (mm) cc_final: 0.8427 (mm) REVERT: x 265 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7283 (t80) REVERT: x 304 TYR cc_start: 0.7658 (p90) cc_final: 0.7403 (p90) REVERT: x 309 GLU cc_start: 0.6889 (mp0) cc_final: 0.6477 (tp30) REVERT: x 346 ASP cc_start: 0.8503 (t0) cc_final: 0.8071 (t0) REVERT: x 373 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7701 (mptt) REVERT: x 488 GLN cc_start: 0.8509 (mt0) cc_final: 0.7823 (pp30) REVERT: x 758 ASP cc_start: 0.8176 (m-30) cc_final: 0.7872 (m-30) REVERT: x 796 GLN cc_start: 0.8163 (mt0) cc_final: 0.7402 (pt0) REVERT: y 90 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: y 109 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8191 (tm) outliers start: 20 outliers final: 7 residues processed: 129 average time/residue: 0.0615 time to fit residues: 10.7177 Evaluate side-chains 105 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4024 r_free = 0.4024 target = 0.163932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115793 restraints weight = 7305.982| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.97 r_work: 0.3281 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6046 Z= 0.163 Angle : 0.602 9.789 8195 Z= 0.307 Chirality : 0.045 0.194 961 Planarity : 0.005 0.038 1008 Dihedral : 7.908 59.090 879 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.39 % Allowed : 10.79 % Favored : 85.82 % 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 are not related in a simple way. whole: -1.27 (0.31), residues: 714 helix: -0.72 (0.27), residues: 306 sheet: -0.02 (0.56), residues: 96 loop : -1.10 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 289 TYR 0.028 0.002 TYR x 304 PHE 0.018 0.002 PHE x 565 TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 6046) covalent geometry : angle 0.60219 / 0.31 ( 8195) hydrogen bonds : bond 0.04280 / 2.71 ( 190) hydrogen bonds : angle 4.53865 / 3.19 ( 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 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: x 235 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8240 (mt-10) REVERT: x 245 MET cc_start: 0.7808 (ttm) cc_final: 0.6763 (mmt) REVERT: x 255 GLN cc_start: 0.8358 (mp10) cc_final: 0.8084 (mp10) REVERT: x 265 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7308 (t80) REVERT: x 309 GLU cc_start: 0.6972 (mp0) cc_final: 0.6553 (tp30) REVERT: x 346 ASP cc_start: 0.8654 (t0) cc_final: 0.8414 (t0) REVERT: x 373 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7647 (mptt) REVERT: x 396 PHE cc_start: 0.7562 (t80) cc_final: 0.7348 (t80) REVERT: x 402 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.8005 (mmm-85) REVERT: x 488 GLN cc_start: 0.8490 (mt0) cc_final: 0.7866 (pp30) REVERT: x 690 ARG cc_start: 0.8367 (tmm-80) cc_final: 0.8164 (tmm-80) REVERT: x 720 SER cc_start: 0.8984 (t) cc_final: 0.8695 (p) REVERT: x 721 ARG cc_start: 0.8843 (ttm-80) cc_final: 0.8637 (ttt90) REVERT: x 758 ASP cc_start: 0.8092 (m-30) cc_final: 0.7645 (m-30) REVERT: x 762 MET cc_start: 0.7515 (mmp) cc_final: 0.7302 (mmp) REVERT: x 796 GLN cc_start: 0.8232 (mt0) cc_final: 0.7517 (pt0) REVERT: x 851 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7763 (mttm) REVERT: y 109 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8132 (tm) outliers start: 22 outliers final: 10 residues processed: 117 average time/residue: 0.0614 time to fit residues: 9.5835 Evaluate side-chains 104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 265 PHE 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 534 THR Chi-restraints excluded: chain x residue 748 SER Chi-restraints excluded: chain x residue 798 MET 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 49 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4032 r_free = 0.4032 target = 0.164696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117202 restraints weight = 7283.539| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.93 r_work: 0.3287 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6046 Z= 0.131 Angle : 0.544 8.497 8195 Z= 0.279 Chirality : 0.044 0.190 961 Planarity : 0.004 0.035 1008 Dihedral : 7.403 60.289 876 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.92 % Favored : 95.94 % Rotamer: Outliers : 3.24 % Allowed : 12.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.31), residues: 714 helix: -0.19 (0.29), residues: 309 sheet: -0.01 (0.56), residues: 96 loop : -0.98 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 289 TYR 0.010 0.001 TYR x 475 PHE 0.018 0.001 PHE x 565 TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 6046) covalent geometry : angle 0.54385 / 0.28 ( 8195) hydrogen bonds : bond 0.03514 / 2.23 ( 190) hydrogen bonds : angle 4.20453 / 2.97 ( 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 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7853 (ttm) cc_final: 0.7213 (mmt) REVERT: x 265 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7356 (t80) REVERT: x 289 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: x 304 TYR cc_start: 0.7661 (p90) cc_final: 0.7451 (p90) REVERT: x 326 MET cc_start: 0.8429 (mtp) cc_final: 0.7980 (mtp) REVERT: x 346 ASP cc_start: 0.8622 (t0) cc_final: 0.8405 (t0) REVERT: x 373 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7578 (mptt) REVERT: x 381 MET cc_start: 0.8489 (tpp) cc_final: 0.8003 (tpp) REVERT: x 488 GLN cc_start: 0.8499 (mt0) cc_final: 0.7926 (pp30) REVERT: x 720 SER cc_start: 0.8983 (t) cc_final: 0.8677 (p) REVERT: x 758 ASP cc_start: 0.8080 (m-30) cc_final: 0.7632 (m-30) REVERT: x 762 MET cc_start: 0.7419 (mmp) cc_final: 0.7197 (mmp) REVERT: x 796 GLN cc_start: 0.8228 (mt0) cc_final: 0.7525 (pt0) REVERT: x 851 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7721 (mttm) REVERT: y 109 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8229 (tm) outliers start: 21 outliers final: 13 residues processed: 115 average time/residue: 0.0666 time to fit residues: 10.1631 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 : 0.193 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4058 r_free = 0.4058 target = 0.166209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118741 restraints weight = 7487.658| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.95 r_work: 0.3328 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6046 Z= 0.103 Angle : 0.522 7.619 8195 Z= 0.269 Chirality : 0.043 0.181 961 Planarity : 0.004 0.033 1008 Dihedral : 7.249 62.741 876 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 2.77 % Allowed : 12.79 % Favored : 84.44 % 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 are not related in a simple way. whole: -0.54 (0.32), residues: 714 helix: 0.13 (0.30), residues: 307 sheet: -0.14 (0.55), residues: 98 loop : -0.82 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG x 495 TYR 0.011 0.001 TYR x 259 PHE 0.013 0.001 PHE x 565 TRP 0.006 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 6046) covalent geometry : angle 0.52222 / 0.27 ( 8195) hydrogen bonds : bond 0.03118 / 1.98 ( 190) hydrogen bonds : angle 4.00402 / 2.85 ( 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 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.145 Fit side-chains REVERT: x 245 MET cc_start: 0.7807 (ttm) cc_final: 0.7239 (mmt) REVERT: x 265 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7442 (t80) REVERT: x 304 TYR cc_start: 0.7677 (p90) cc_final: 0.7385 (p90) REVERT: x 326 MET cc_start: 0.8363 (mtp) cc_final: 0.7885 (mtp) REVERT: x 339 LYS cc_start: 0.8724 (mttt) cc_final: 0.8451 (mtpt) REVERT: x 346 ASP cc_start: 0.8622 (t0) cc_final: 0.8267 (t0) REVERT: x 347 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8467 (mm-30) REVERT: x 373 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7700 (mptt) REVERT: x 380 THR cc_start: 0.8972 (p) cc_final: 0.8584 (p) REVERT: x 381 MET cc_start: 0.8378 (tpp) cc_final: 0.7799 (tpp) REVERT: x 528 VAL cc_start: 0.8041 (t) cc_final: 0.7834 (m) REVERT: x 720 SER cc_start: 0.8947 (t) cc_final: 0.8700 (p) REVERT: x 758 ASP cc_start: 0.8028 (m-30) cc_final: 0.7584 (m-30) REVERT: x 796 GLN cc_start: 0.8228 (mt0) cc_final: 0.7461 (pt0) REVERT: x 851 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7960 (mmmm) REVERT: y 90 GLU cc_start: 0.7573 (tp30) cc_final: 0.7171 (tp30) REVERT: y 109 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (tm) outliers start: 18 outliers final: 9 residues processed: 116 average time/residue: 0.0593 time to fit residues: 9.3277 Evaluate side-chains 108 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 47 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4044 r_free = 0.4044 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117096 restraints weight = 7430.201| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.93 r_work: 0.3303 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6046 Z= 0.129 Angle : 0.536 7.768 8195 Z= 0.276 Chirality : 0.043 0.160 961 Planarity : 0.004 0.030 1008 Dihedral : 7.118 61.242 874 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 3.24 % Allowed : 13.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.32), residues: 714 helix: 0.30 (0.30), residues: 307 sheet: -0.15 (0.55), residues: 98 loop : -0.77 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 289 TYR 0.010 0.001 TYR x 403 PHE 0.009 0.001 PHE x 562 TRP 0.009 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6046) covalent geometry : angle 0.53634 / 0.28 ( 8195) hydrogen bonds : bond 0.03359 / 2.14 ( 190) hydrogen bonds : angle 4.03794 / 2.86 ( 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 115 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.166 Fit side-chains REVERT: x 245 MET cc_start: 0.7796 (ttm) cc_final: 0.7193 (mmt) REVERT: x 265 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7436 (t80) REVERT: x 304 TYR cc_start: 0.7721 (p90) cc_final: 0.7378 (p90) REVERT: x 309 GLU cc_start: 0.7016 (mp0) cc_final: 0.6064 (tp30) REVERT: x 326 MET cc_start: 0.8385 (mtp) cc_final: 0.7870 (mtp) REVERT: x 339 LYS cc_start: 0.8708 (mttt) cc_final: 0.8446 (mtpt) REVERT: x 373 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7754 (mptt) REVERT: x 380 THR cc_start: 0.9012 (p) cc_final: 0.8580 (p) REVERT: x 381 MET cc_start: 0.8449 (tpp) cc_final: 0.7954 (tpp) REVERT: x 528 VAL cc_start: 0.8053 (t) cc_final: 0.7819 (m) REVERT: x 720 SER cc_start: 0.8976 (t) cc_final: 0.8694 (p) REVERT: x 758 ASP cc_start: 0.8072 (m-30) cc_final: 0.7597 (m-30) REVERT: x 796 GLN cc_start: 0.8247 (mt0) cc_final: 0.7533 (pt0) REVERT: x 851 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8024 (mmmm) REVERT: y 90 GLU cc_start: 0.7531 (tp30) cc_final: 0.7105 (tp30) REVERT: y 96 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7392 (mt-10) REVERT: y 109 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8230 (tm) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.0648 time to fit residues: 9.8038 Evaluate side-chains 108 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 0.0010 chunk 29 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 overall best weight: 1.1888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4039 r_free = 0.4039 target = 0.164172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116569 restraints weight = 7452.045| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.93 r_work: 0.3295 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6046 Z= 0.141 Angle : 0.540 7.160 8195 Z= 0.278 Chirality : 0.043 0.170 961 Planarity : 0.004 0.030 1008 Dihedral : 7.046 58.326 874 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.93 % Allowed : 13.87 % 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 are not related in a simple way. whole: -0.34 (0.32), residues: 714 helix: 0.40 (0.30), residues: 307 sheet: -0.04 (0.56), residues: 96 loop : -0.82 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 495 TYR 0.011 0.001 TYR x 403 PHE 0.013 0.001 PHE x 565 TRP 0.009 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 6046) covalent geometry : angle 0.54014 / 0.28 ( 8195) hydrogen bonds : bond 0.03426 / 2.17 ( 190) hydrogen bonds : angle 4.03392 / 2.86 ( 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 : 0.190 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7761 (ttm) cc_final: 0.7198 (mmt) REVERT: x 265 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7440 (t80) REVERT: x 289 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7361 (mtm-85) REVERT: x 304 TYR cc_start: 0.7751 (p90) cc_final: 0.7427 (p90) REVERT: x 326 MET cc_start: 0.8404 (mtp) cc_final: 0.7850 (mtp) REVERT: x 339 LYS cc_start: 0.8692 (mttt) cc_final: 0.8434 (mtpt) REVERT: x 346 ASP cc_start: 0.8631 (t0) cc_final: 0.8309 (t0) REVERT: x 373 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7772 (mptt) REVERT: x 380 THR cc_start: 0.9013 (p) cc_final: 0.8604 (p) REVERT: x 381 MET cc_start: 0.8534 (tpp) cc_final: 0.8068 (tpp) REVERT: x 720 SER cc_start: 0.9003 (t) cc_final: 0.8690 (p) REVERT: x 758 ASP cc_start: 0.8047 (m-30) cc_final: 0.7587 (m-30) REVERT: x 796 GLN cc_start: 0.8271 (mt0) cc_final: 0.7550 (pt0) REVERT: x 851 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7998 (mmmm) REVERT: y 90 GLU cc_start: 0.7565 (tp30) cc_final: 0.7147 (tp30) outliers start: 19 outliers final: 15 residues processed: 108 average time/residue: 0.0688 time to fit residues: 9.9881 Evaluate side-chains 106 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.0270 chunk 48 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4034 r_free = 0.4034 target = 0.161507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115108 restraints weight = 7574.043| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.85 r_work: 0.3310 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3787 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= 0.107 Angle : 0.525 7.239 8195 Z= 0.270 Chirality : 0.042 0.167 961 Planarity : 0.004 0.030 1008 Dihedral : 6.971 59.505 874 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 2.77 % Allowed : 14.48 % 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 are not related in a simple way. whole: -0.17 (0.32), residues: 714 helix: 0.55 (0.30), residues: 308 sheet: -0.05 (0.56), residues: 98 loop : -0.72 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 495 TYR 0.011 0.001 TYR x 321 PHE 0.009 0.001 PHE x 562 TRP 0.009 0.001 TRP x 568 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6046) covalent geometry : angle 0.52453 / 0.27 ( 8195) hydrogen bonds : bond 0.03009 / 1.92 ( 190) hydrogen bonds : angle 3.92589 / 2.78 ( 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 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7791 (ttm) cc_final: 0.7433 (mmt) REVERT: x 265 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7423 (t80) REVERT: x 304 TYR cc_start: 0.7819 (p90) cc_final: 0.7375 (p90) REVERT: x 326 MET cc_start: 0.8336 (mtp) cc_final: 0.7795 (mtp) REVERT: x 346 ASP cc_start: 0.8525 (t0) cc_final: 0.8253 (t0) REVERT: x 381 MET cc_start: 0.8522 (tpp) cc_final: 0.8195 (tpp) REVERT: x 720 SER cc_start: 0.9019 (t) cc_final: 0.8728 (p) REVERT: x 758 ASP cc_start: 0.8029 (m-30) cc_final: 0.7567 (m-30) REVERT: x 796 GLN cc_start: 0.8313 (mt0) cc_final: 0.7617 (pt0) REVERT: x 858 MET cc_start: 0.8985 (mmm) cc_final: 0.8484 (tpt) REVERT: y 90 GLU cc_start: 0.7529 (tp30) cc_final: 0.7167 (tp30) REVERT: y 109 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8265 (tm) outliers start: 18 outliers final: 11 residues processed: 113 average time/residue: 0.0728 time to fit residues: 11.1875 Evaluate side-chains 102 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4014 r_free = 0.4014 target = 0.159660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.113438 restraints weight = 7671.489| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.85 r_work: 0.3292 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6046 Z= 0.140 Angle : 0.556 7.193 8195 Z= 0.285 Chirality : 0.043 0.170 961 Planarity : 0.004 0.031 1008 Dihedral : 6.979 57.955 874 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 2.77 % Allowed : 15.41 % Favored : 81.82 % 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 are not related in a simple way. whole: -0.14 (0.32), residues: 714 helix: 0.58 (0.30), residues: 310 sheet: -0.32 (0.54), residues: 108 loop : -0.61 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 495 TYR 0.011 0.001 TYR x 403 PHE 0.012 0.001 PHE x 565 TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 6046) covalent geometry : angle 0.55608 / 0.29 ( 8195) hydrogen bonds : bond 0.03323 / 2.13 ( 190) hydrogen bonds : angle 3.96068 / 2.80 ( 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 107 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: x 227 GLN cc_start: 0.8648 (mp10) cc_final: 0.8448 (pt0) REVERT: x 245 MET cc_start: 0.7815 (ttm) cc_final: 0.7319 (mmt) REVERT: x 255 GLN cc_start: 0.8346 (mp10) cc_final: 0.8052 (mp10) REVERT: x 265 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6968 (t80) REVERT: x 304 TYR cc_start: 0.7856 (p90) cc_final: 0.7418 (p90) REVERT: x 326 MET cc_start: 0.8398 (mtp) cc_final: 0.7830 (mtp) REVERT: x 346 ASP cc_start: 0.8572 (t0) cc_final: 0.8288 (t0) REVERT: x 373 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (mppt) REVERT: x 380 THR cc_start: 0.8996 (p) cc_final: 0.8623 (p) REVERT: x 381 MET cc_start: 0.8525 (tpp) cc_final: 0.8199 (tpp) REVERT: x 720 SER cc_start: 0.9012 (t) cc_final: 0.8733 (p) REVERT: x 721 ARG cc_start: 0.9099 (ttt90) cc_final: 0.8852 (tpt-90) REVERT: x 758 ASP cc_start: 0.8031 (m-30) cc_final: 0.7591 (m-30) REVERT: x 796 GLN cc_start: 0.8334 (mt0) cc_final: 0.7638 (pt0) REVERT: x 858 MET cc_start: 0.8984 (mmm) cc_final: 0.8503 (tpt) REVERT: y 90 GLU cc_start: 0.7536 (tp30) cc_final: 0.7199 (tp30) REVERT: y 109 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8296 (tm) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.0702 time to fit residues: 9.9740 Evaluate side-chains 101 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.157352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110988 restraints weight = 7736.474| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.85 r_work: 0.3257 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6046 Z= 0.191 Angle : 0.584 7.359 8195 Z= 0.302 Chirality : 0.045 0.173 961 Planarity : 0.004 0.037 1008 Dihedral : 7.072 53.494 874 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % 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 are not related in a simple way. whole: -0.28 (0.32), residues: 714 helix: 0.49 (0.30), residues: 310 sheet: -0.48 (0.53), residues: 108 loop : -0.66 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 495 TYR 0.012 0.002 TYR x 475 PHE 0.026 0.002 PHE x 396 TRP 0.009 0.001 TRP x 568 HIS 0.004 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 ( 6046) covalent geometry : angle 0.58358 / 0.30 ( 8195) hydrogen bonds : bond 0.03766 / 2.39 ( 190) hydrogen bonds : angle 4.14504 / 2.94 ( 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: 16 poor density : 89 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: x 245 MET cc_start: 0.7849 (ttm) cc_final: 0.7372 (mmt) REVERT: x 255 GLN cc_start: 0.8407 (mp10) cc_final: 0.8137 (mp10) REVERT: x 265 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7438 (t80) REVERT: x 304 TYR cc_start: 0.7867 (p90) cc_final: 0.7521 (p90) REVERT: x 326 MET cc_start: 0.8486 (mtp) cc_final: 0.7904 (mtp) REVERT: x 346 ASP cc_start: 0.8621 (t0) cc_final: 0.8335 (t0) REVERT: x 380 THR cc_start: 0.9030 (p) cc_final: 0.8505 (m) REVERT: x 381 MET cc_start: 0.8582 (tpp) cc_final: 0.8126 (tpp) REVERT: x 397 ASN cc_start: 0.9033 (t0) cc_final: 0.8625 (t0) REVERT: x 720 SER cc_start: 0.8993 (t) cc_final: 0.8693 (p) REVERT: x 758 ASP cc_start: 0.8009 (m-30) cc_final: 0.7569 (m-30) REVERT: x 796 GLN cc_start: 0.8370 (mt0) cc_final: 0.7672 (pt0) REVERT: x 858 MET cc_start: 0.8995 (mmm) cc_final: 0.8498 (tpt) REVERT: y 90 GLU cc_start: 0.7580 (tp30) cc_final: 0.7227 (tp30) REVERT: y 109 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8286 (tm) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.0590 time to fit residues: 8.5282 Evaluate side-chains 100 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 66 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 239 ASN x 382 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116070 restraints weight = 7591.989| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.86 r_work: 0.3320 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 6046 Z= 0.103 Angle : 0.542 7.256 8195 Z= 0.277 Chirality : 0.042 0.164 961 Planarity : 0.004 0.033 1008 Dihedral : 6.903 57.217 874 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.06 % Favored : 95.80 % Rotamer: Outliers : 2.00 % Allowed : 16.49 % 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 are not related in a simple way. whole: -0.08 (0.32), residues: 714 helix: 0.76 (0.30), residues: 303 sheet: -0.56 (0.52), residues: 111 loop : -0.58 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 495 TYR 0.010 0.001 TYR x 321 PHE 0.043 0.001 PHE x 396 TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.10 ( 6046) covalent geometry : angle 0.54204 / 0.28 ( 8195) hydrogen bonds : bond 0.02837 / 1.82 ( 190) hydrogen bonds : angle 3.86318 / 2.74 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.73 seconds wall clock time: 28 minutes 28.13 seconds (1708.13 seconds total)