Starting phenix.real_space_refine on Tue Mar 3 17:45:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln8_0927/03_2026/6ln8_0927.cif" } resolution = 3.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 57 5.16 5 Be 1 3.05 5 C 4932 2.51 5 N 1294 2.21 5 O 1451 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7739 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 957} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.85, per 1000 atoms: 0.24 Number of scatterers: 7739 At special positions: 0 Unit cell: (88.395, 92.13, 145.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 57 16.00 Mg 1 11.99 F 3 9.00 O 1451 8.00 N 1294 7.00 C 4932 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 305.4 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 54.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.713A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.677A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 84 through 118 removed outlier: 5.083A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.638A pdb=" N ALA A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 276 Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.320A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.632A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.929A pdb=" N ASN A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 4.468A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.090A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.735A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 661 through 672 Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.739A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 739 through 781 removed outlier: 3.872A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.938A pdb=" N TRP A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 814 through 818 removed outlier: 4.042A pdb=" N LYS A 818 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.844A pdb=" N ILE A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.601A pdb=" N LYS A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.471A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 951 through 956 removed outlier: 3.599A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.981A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 12.144A pdb=" N MET A 126 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ALA A 154 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 218 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 168 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.479A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 213 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.205A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.639A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.183A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS A 524 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 592 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 12.816A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 493 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 487 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 495 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 428 439 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2532 1.34 - 1.46: 1398 1.46 - 1.58: 3862 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7880 Sorted by residual: bond pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" F3 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C ASP A 398 " pdb=" O ASP A 398 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.30e-02 5.92e+03 9.31e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 6.89e-01 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 10644 2.78 - 5.56: 46 5.56 - 8.34: 1 8.34 - 11.12: 1 11.12 - 13.90: 1 Bond angle restraints: 10693 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.06 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.98 10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" C ASP A 398 " ideal model delta sigma weight residual 112.13 107.72 4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N THR A 358 " pdb=" CA THR A 358 " pdb=" C THR A 358 " ideal model delta sigma weight residual 110.53 106.96 3.57 1.29e+00 6.01e-01 7.65e+00 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.30 7.61 3.00e+00 1.11e-01 6.44e+00 ... (remaining 10688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4279 16.00 - 32.01: 397 32.01 - 48.01: 89 48.01 - 64.01: 7 64.01 - 80.01: 5 Dihedral angle restraints: 4777 sinusoidal: 1882 harmonic: 2895 Sorted by residual: dihedral pdb=" CA LEU A 947 " pdb=" C LEU A 947 " pdb=" N TYR A 948 " pdb=" CA TYR A 948 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 357 " pdb=" C THR A 357 " pdb=" N THR A 358 " pdb=" CA THR A 358 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CB MET A 908 " pdb=" CG MET A 908 " pdb=" SD MET A 908 " pdb=" CE MET A 908 " ideal model delta sinusoidal sigma weight residual 60.00 112.21 -52.21 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 735 0.027 - 0.055: 345 0.055 - 0.082: 102 0.082 - 0.110: 60 0.110 - 0.137: 17 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE A 307 " pdb=" N ILE A 307 " pdb=" C ILE A 307 " pdb=" CB ILE A 307 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 621 " pdb=" N ILE A 621 " pdb=" C ILE A 621 " pdb=" CB ILE A 621 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1256 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 975 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU A 796 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 952 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 953 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 953 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 953 " 0.021 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 61 2.62 - 3.19: 7035 3.19 - 3.76: 12017 3.76 - 4.33: 16964 4.33 - 4.90: 28144 Nonbonded interactions: 64221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F1 BEF A2001 " pdb="MG MG A2002 " model vdw 2.059 2.120 nonbonded pdb=" OD2 ASP A 351 " pdb=" F1 BEF A2001 " model vdw 2.085 2.990 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.097 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.101 2.170 ... (remaining 64216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.270 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.011 0.925 7881 Z= 1.054 Angle : 0.562 13.901 10693 Z= 0.320 Chirality : 0.039 0.137 1259 Planarity : 0.004 0.041 1362 Dihedral : 12.814 80.014 2901 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.71 (0.22), residues: 997 helix: -1.61 (0.20), residues: 506 sheet: -1.80 (0.43), residues: 105 loop : -1.82 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.015 0.001 TYR A 836 PHE 0.016 0.001 PHE A 759 TRP 0.006 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7880) covalent geometry : angle 0.56235 (10693) hydrogen bonds : bond 0.17915 ( 415) hydrogen bonds : angle 7.14433 ( 1269) Misc. bond : bond 0.92519 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.241 Fit side-chains REVERT: A 63 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7612 (mtm-85) REVERT: A 128 LYS cc_start: 0.8284 (mttt) cc_final: 0.8037 (mtmm) REVERT: A 140 ILE cc_start: 0.8162 (pt) cc_final: 0.7732 (pt) REVERT: A 545 MET cc_start: 0.7956 (mmm) cc_final: 0.7627 (tpp) REVERT: A 586 TYR cc_start: 0.6963 (m-10) cc_final: 0.6597 (m-80) REVERT: A 732 MET cc_start: 0.8480 (ttm) cc_final: 0.8260 (ttt) REVERT: A 816 MET cc_start: 0.7378 (mmm) cc_final: 0.6963 (mmm) REVERT: A 1028 TRP cc_start: 0.7329 (t60) cc_final: 0.6918 (t60) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1179 time to fit residues: 21.7752 Evaluate side-chains 113 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 177 GLN A 428 ASN A 582 ASN A 615 GLN A 671 ASN A 682 HIS A 868 GLN A 943 HIS A 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132406 restraints weight = 8327.821| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.81 r_work: 0.3287 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7881 Z= 0.141 Angle : 0.507 5.502 10693 Z= 0.266 Chirality : 0.041 0.147 1259 Planarity : 0.004 0.042 1362 Dihedral : 3.955 16.875 1061 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.82 % Allowed : 11.01 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.25), residues: 997 helix: -0.14 (0.22), residues: 520 sheet: -1.57 (0.43), residues: 105 loop : -1.08 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 666 TYR 0.017 0.002 TYR A 762 PHE 0.026 0.001 PHE A 759 TRP 0.012 0.001 TRP A 831 HIS 0.002 0.000 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7880) covalent geometry : angle 0.50736 (10693) hydrogen bonds : bond 0.04723 ( 415) hydrogen bonds : angle 4.56134 ( 1269) Misc. bond : bond 0.00152 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.269 Fit side-chains REVERT: A 63 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7403 (mtm-85) REVERT: A 128 LYS cc_start: 0.8770 (mttt) cc_final: 0.8482 (mtmm) REVERT: A 140 ILE cc_start: 0.8126 (pt) cc_final: 0.7703 (pt) REVERT: A 143 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7801 (mtmm) REVERT: A 297 LYS cc_start: 0.6825 (mtpp) cc_final: 0.6579 (mttp) REVERT: A 518 GLU cc_start: 0.8341 (pp20) cc_final: 0.7774 (pp20) REVERT: A 536 MET cc_start: 0.7395 (ttm) cc_final: 0.6865 (ttm) REVERT: A 586 TYR cc_start: 0.7052 (m-10) cc_final: 0.6640 (m-80) REVERT: A 816 MET cc_start: 0.7969 (mmm) cc_final: 0.7599 (mmm) REVERT: A 1028 TRP cc_start: 0.7580 (t60) cc_final: 0.6969 (t60) outliers start: 7 outliers final: 7 residues processed: 128 average time/residue: 0.1128 time to fit residues: 18.7130 Evaluate side-chains 115 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.175200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132508 restraints weight = 8346.315| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.80 r_work: 0.3287 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7881 Z= 0.127 Angle : 0.489 6.147 10693 Z= 0.255 Chirality : 0.041 0.146 1259 Planarity : 0.004 0.045 1362 Dihedral : 3.850 17.502 1061 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.99 % Allowed : 13.23 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.26), residues: 997 helix: 0.38 (0.23), residues: 519 sheet: -1.45 (0.43), residues: 103 loop : -0.83 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.014 0.001 TYR A 762 PHE 0.026 0.001 PHE A 759 TRP 0.010 0.001 TRP A 927 HIS 0.002 0.001 HIS A 871 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7880) covalent geometry : angle 0.48941 (10693) hydrogen bonds : bond 0.04312 ( 415) hydrogen bonds : angle 4.28070 ( 1269) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.270 Fit side-chains REVERT: A 63 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7373 (mtm-85) REVERT: A 120 LYS cc_start: 0.7397 (mttp) cc_final: 0.7025 (mmtp) REVERT: A 128 LYS cc_start: 0.8774 (mttt) cc_final: 0.8498 (mtmm) REVERT: A 140 ILE cc_start: 0.8156 (pt) cc_final: 0.7724 (pt) REVERT: A 143 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7846 (mtmm) REVERT: A 297 LYS cc_start: 0.6935 (mtpp) cc_final: 0.6675 (mttp) REVERT: A 518 GLU cc_start: 0.8348 (pp20) cc_final: 0.7831 (pp20) REVERT: A 536 MET cc_start: 0.7367 (ttm) cc_final: 0.6990 (ttm) REVERT: A 542 GLN cc_start: 0.7251 (pp30) cc_final: 0.7038 (pp30) REVERT: A 549 ARG cc_start: 0.7566 (mpp80) cc_final: 0.7312 (mpp80) REVERT: A 586 TYR cc_start: 0.7094 (m-10) cc_final: 0.6789 (m-80) REVERT: A 714 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: A 816 MET cc_start: 0.7993 (mmm) cc_final: 0.7619 (mmm) REVERT: A 940 MET cc_start: 0.7769 (mmt) cc_final: 0.7543 (tpp) REVERT: A 1028 TRP cc_start: 0.7593 (t60) cc_final: 0.6976 (t60) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.1158 time to fit residues: 19.5219 Evaluate side-chains 119 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN A 767 ASN A 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.172385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130746 restraints weight = 8534.631| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.82 r_work: 0.3243 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7881 Z= 0.197 Angle : 0.552 6.181 10693 Z= 0.287 Chirality : 0.043 0.159 1259 Planarity : 0.004 0.046 1362 Dihedral : 4.063 18.346 1061 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.69 % Allowed : 14.29 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.26), residues: 997 helix: 0.32 (0.23), residues: 515 sheet: -1.48 (0.43), residues: 105 loop : -0.77 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 655 TYR 0.016 0.002 TYR A 762 PHE 0.025 0.002 PHE A 759 TRP 0.008 0.001 TRP A 831 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 7880) covalent geometry : angle 0.55209 (10693) hydrogen bonds : bond 0.04786 ( 415) hydrogen bonds : angle 4.36691 ( 1269) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.344 Fit side-chains REVERT: A 63 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7567 (mtm-85) REVERT: A 143 LYS cc_start: 0.8126 (mtmt) cc_final: 0.7911 (mtmm) REVERT: A 297 LYS cc_start: 0.7031 (mtpp) cc_final: 0.6761 (mttp) REVERT: A 518 GLU cc_start: 0.8377 (pp20) cc_final: 0.7889 (pp20) REVERT: A 583 PHE cc_start: 0.7197 (m-80) cc_final: 0.6776 (m-80) REVERT: A 586 TYR cc_start: 0.7319 (m-10) cc_final: 0.7089 (m-80) REVERT: A 791 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 816 MET cc_start: 0.8218 (mmm) cc_final: 0.7753 (mmm) REVERT: A 836 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.5811 (p90) REVERT: A 1028 TRP cc_start: 0.7584 (t60) cc_final: 0.6984 (t60) outliers start: 23 outliers final: 15 residues processed: 136 average time/residue: 0.1188 time to fit residues: 20.7203 Evaluate side-chains 127 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 6 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 767 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133703 restraints weight = 8351.627| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.79 r_work: 0.3309 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7881 Z= 0.105 Angle : 0.474 6.282 10693 Z= 0.246 Chirality : 0.040 0.142 1259 Planarity : 0.004 0.047 1362 Dihedral : 3.825 17.905 1061 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.64 % Allowed : 15.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.26), residues: 997 helix: 0.70 (0.23), residues: 520 sheet: -1.41 (0.41), residues: 115 loop : -0.62 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 655 TYR 0.014 0.001 TYR A 990 PHE 0.024 0.001 PHE A 759 TRP 0.010 0.001 TRP A 854 HIS 0.001 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7880) covalent geometry : angle 0.47352 (10693) hydrogen bonds : bond 0.03908 ( 415) hydrogen bonds : angle 4.10025 ( 1269) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.268 Fit side-chains REVERT: A 63 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7502 (mtm-85) REVERT: A 120 LYS cc_start: 0.7420 (mttp) cc_final: 0.7097 (mmtp) REVERT: A 140 ILE cc_start: 0.8126 (pt) cc_final: 0.7693 (pt) REVERT: A 297 LYS cc_start: 0.6916 (mtpp) cc_final: 0.6663 (mttp) REVERT: A 518 GLU cc_start: 0.8344 (pp20) cc_final: 0.7851 (pp20) REVERT: A 549 ARG cc_start: 0.7474 (mpp80) cc_final: 0.7195 (mpp80) REVERT: A 583 PHE cc_start: 0.7147 (m-80) cc_final: 0.6729 (m-80) REVERT: A 761 ARG cc_start: 0.8252 (mtm110) cc_final: 0.8003 (mtp-110) REVERT: A 816 MET cc_start: 0.8101 (mmm) cc_final: 0.7737 (mmm) REVERT: A 836 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5695 (p90) REVERT: A 940 MET cc_start: 0.7782 (mmt) cc_final: 0.7526 (tpp) REVERT: A 955 ILE cc_start: 0.7010 (mt) cc_final: 0.6803 (tp) REVERT: A 1028 TRP cc_start: 0.7605 (t60) cc_final: 0.7045 (t60) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 0.1148 time to fit residues: 19.9231 Evaluate side-chains 130 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.177253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134949 restraints weight = 8355.128| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.78 r_work: 0.3327 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7881 Z= 0.100 Angle : 0.468 6.182 10693 Z= 0.242 Chirality : 0.040 0.141 1259 Planarity : 0.003 0.048 1362 Dihedral : 3.709 17.887 1061 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.04 % Allowed : 15.81 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.26), residues: 997 helix: 0.99 (0.24), residues: 513 sheet: -1.04 (0.45), residues: 104 loop : -0.53 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 666 TYR 0.018 0.002 TYR A 427 PHE 0.025 0.001 PHE A 759 TRP 0.011 0.001 TRP A 854 HIS 0.001 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 7880) covalent geometry : angle 0.46785 (10693) hydrogen bonds : bond 0.03683 ( 415) hydrogen bonds : angle 3.99872 ( 1269) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7448 (mttp) cc_final: 0.7148 (mmtp) REVERT: A 140 ILE cc_start: 0.8153 (pt) cc_final: 0.7747 (pt) REVERT: A 143 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7873 (mtmm) REVERT: A 297 LYS cc_start: 0.6814 (mtpp) cc_final: 0.6583 (mttp) REVERT: A 332 ILE cc_start: 0.8901 (mm) cc_final: 0.8574 (mt) REVERT: A 518 GLU cc_start: 0.8367 (pp20) cc_final: 0.7875 (pp20) REVERT: A 549 ARG cc_start: 0.7447 (mpp80) cc_final: 0.7238 (mpp80) REVERT: A 583 PHE cc_start: 0.7426 (m-80) cc_final: 0.6895 (m-80) REVERT: A 586 TYR cc_start: 0.7247 (m-80) cc_final: 0.6709 (m-80) REVERT: A 761 ARG cc_start: 0.8223 (mtm110) cc_final: 0.8010 (mtp-110) REVERT: A 816 MET cc_start: 0.8144 (mmm) cc_final: 0.7746 (mmm) REVERT: A 836 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5651 (p90) REVERT: A 940 MET cc_start: 0.7795 (mmt) cc_final: 0.7585 (tpp) REVERT: A 1028 TRP cc_start: 0.7609 (t60) cc_final: 0.7051 (t60) outliers start: 26 outliers final: 17 residues processed: 145 average time/residue: 0.1075 time to fit residues: 20.4861 Evaluate side-chains 136 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.2980 chunk 56 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.177894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135844 restraints weight = 8293.389| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.76 r_work: 0.3337 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7881 Z= 0.099 Angle : 0.470 6.433 10693 Z= 0.242 Chirality : 0.040 0.182 1259 Planarity : 0.004 0.043 1362 Dihedral : 3.671 17.674 1061 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.34 % Allowed : 17.68 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.27), residues: 997 helix: 0.98 (0.24), residues: 525 sheet: -0.98 (0.45), residues: 104 loop : -0.51 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.015 0.002 TYR A 990 PHE 0.024 0.001 PHE A 759 TRP 0.012 0.001 TRP A 927 HIS 0.002 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7880) covalent geometry : angle 0.47033 (10693) hydrogen bonds : bond 0.03533 ( 415) hydrogen bonds : angle 3.92782 ( 1269) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7478 (mttp) cc_final: 0.7073 (mmtp) REVERT: A 140 ILE cc_start: 0.8124 (pt) cc_final: 0.7745 (pt) REVERT: A 143 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7844 (mtmm) REVERT: A 266 LEU cc_start: 0.8103 (tt) cc_final: 0.7620 (tp) REVERT: A 297 LYS cc_start: 0.6769 (mtpp) cc_final: 0.6505 (mttp) REVERT: A 332 ILE cc_start: 0.8874 (mm) cc_final: 0.8560 (mt) REVERT: A 518 GLU cc_start: 0.8357 (pp20) cc_final: 0.7896 (pp20) REVERT: A 526 HIS cc_start: 0.7406 (m-70) cc_final: 0.7025 (m-70) REVERT: A 536 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7434 (ttm) REVERT: A 549 ARG cc_start: 0.7430 (mpp80) cc_final: 0.6923 (mpp80) REVERT: A 583 PHE cc_start: 0.7516 (m-80) cc_final: 0.7127 (m-80) REVERT: A 586 TYR cc_start: 0.7350 (m-80) cc_final: 0.7091 (m-80) REVERT: A 761 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7979 (mtp-110) REVERT: A 816 MET cc_start: 0.8075 (mmm) cc_final: 0.7719 (mmm) REVERT: A 836 TYR cc_start: 0.6784 (OUTLIER) cc_final: 0.5667 (p90) REVERT: A 1028 TRP cc_start: 0.7616 (t60) cc_final: 0.7051 (t60) outliers start: 20 outliers final: 17 residues processed: 141 average time/residue: 0.1058 time to fit residues: 19.6617 Evaluate side-chains 136 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 0.0470 chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.177222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134632 restraints weight = 8435.015| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.82 r_work: 0.3320 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7881 Z= 0.112 Angle : 0.485 6.096 10693 Z= 0.249 Chirality : 0.041 0.180 1259 Planarity : 0.004 0.044 1362 Dihedral : 3.694 17.740 1061 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.46 % Allowed : 17.80 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.27), residues: 997 helix: 1.03 (0.24), residues: 520 sheet: -1.01 (0.45), residues: 104 loop : -0.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.014 0.002 TYR A 990 PHE 0.024 0.001 PHE A 759 TRP 0.010 0.001 TRP A 927 HIS 0.001 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7880) covalent geometry : angle 0.48479 (10693) hydrogen bonds : bond 0.03673 ( 415) hydrogen bonds : angle 3.95750 ( 1269) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7472 (mttp) cc_final: 0.7075 (mmtp) REVERT: A 140 ILE cc_start: 0.8114 (pt) cc_final: 0.7725 (pt) REVERT: A 297 LYS cc_start: 0.6781 (mtpp) cc_final: 0.6530 (mttp) REVERT: A 332 ILE cc_start: 0.8909 (mm) cc_final: 0.8595 (mt) REVERT: A 518 GLU cc_start: 0.8415 (pp20) cc_final: 0.7924 (pp20) REVERT: A 526 HIS cc_start: 0.7433 (m-70) cc_final: 0.7045 (m-70) REVERT: A 536 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7431 (ttm) REVERT: A 583 PHE cc_start: 0.7518 (m-80) cc_final: 0.7134 (m-80) REVERT: A 714 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: A 761 ARG cc_start: 0.8265 (mtm110) cc_final: 0.8043 (mtp-110) REVERT: A 816 MET cc_start: 0.8124 (mmm) cc_final: 0.7747 (mmm) REVERT: A 836 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.5638 (p90) REVERT: A 1028 TRP cc_start: 0.7665 (t60) cc_final: 0.7075 (t60) outliers start: 21 outliers final: 16 residues processed: 131 average time/residue: 0.1025 time to fit residues: 17.6485 Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 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 = 0.3978 r_free = 0.3978 target = 0.177096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134821 restraints weight = 8384.871| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.80 r_work: 0.3306 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7881 Z= 0.109 Angle : 0.488 7.908 10693 Z= 0.250 Chirality : 0.041 0.160 1259 Planarity : 0.004 0.048 1362 Dihedral : 3.691 17.535 1061 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.69 % Allowed : 17.45 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.27), residues: 997 helix: 1.14 (0.24), residues: 514 sheet: -1.02 (0.45), residues: 104 loop : -0.48 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.018 0.002 TYR A 586 PHE 0.024 0.001 PHE A 759 TRP 0.011 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7880) covalent geometry : angle 0.48808 (10693) hydrogen bonds : bond 0.03634 ( 415) hydrogen bonds : angle 3.95130 ( 1269) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7473 (mttp) cc_final: 0.7060 (mmtp) REVERT: A 140 ILE cc_start: 0.8119 (pt) cc_final: 0.7741 (pt) REVERT: A 297 LYS cc_start: 0.6789 (mtpp) cc_final: 0.6539 (mttp) REVERT: A 518 GLU cc_start: 0.8447 (pp20) cc_final: 0.7948 (pp20) REVERT: A 526 HIS cc_start: 0.7441 (m-70) cc_final: 0.7106 (m-70) REVERT: A 536 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7388 (ttm) REVERT: A 583 PHE cc_start: 0.7485 (m-80) cc_final: 0.7036 (m-80) REVERT: A 586 TYR cc_start: 0.7199 (m-80) cc_final: 0.6746 (m-80) REVERT: A 714 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: A 761 ARG cc_start: 0.8268 (mtm110) cc_final: 0.8056 (mtp-110) REVERT: A 816 MET cc_start: 0.8105 (mmm) cc_final: 0.7760 (mmm) REVERT: A 836 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5690 (p90) REVERT: A 1028 TRP cc_start: 0.7673 (t60) cc_final: 0.7082 (t60) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.1040 time to fit residues: 17.8989 Evaluate side-chains 131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.178052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135831 restraints weight = 8333.916| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.79 r_work: 0.3336 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7881 Z= 0.104 Angle : 0.491 7.750 10693 Z= 0.252 Chirality : 0.041 0.157 1259 Planarity : 0.004 0.048 1362 Dihedral : 3.651 17.308 1061 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 17.45 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.27), residues: 997 helix: 1.24 (0.24), residues: 512 sheet: -0.95 (0.46), residues: 104 loop : -0.47 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.016 0.002 TYR A 586 PHE 0.024 0.001 PHE A 759 TRP 0.011 0.001 TRP A 927 HIS 0.001 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7880) covalent geometry : angle 0.49089 (10693) hydrogen bonds : bond 0.03541 ( 415) hydrogen bonds : angle 3.94015 ( 1269) Misc. bond : bond 0.00051 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7463 (mttp) cc_final: 0.7076 (mmtp) REVERT: A 140 ILE cc_start: 0.8107 (pt) cc_final: 0.7719 (pt) REVERT: A 297 LYS cc_start: 0.6765 (mtpp) cc_final: 0.6503 (mttp) REVERT: A 332 ILE cc_start: 0.8899 (mm) cc_final: 0.8598 (mt) REVERT: A 518 GLU cc_start: 0.8423 (pp20) cc_final: 0.7919 (pp20) REVERT: A 536 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7379 (ttm) REVERT: A 583 PHE cc_start: 0.7450 (m-80) cc_final: 0.7150 (m-80) REVERT: A 714 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: A 761 ARG cc_start: 0.8223 (mtm110) cc_final: 0.8008 (mtp-110) REVERT: A 816 MET cc_start: 0.8136 (mmm) cc_final: 0.7871 (mmm) REVERT: A 836 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5686 (p90) REVERT: A 1028 TRP cc_start: 0.7676 (t60) cc_final: 0.7072 (t60) outliers start: 22 outliers final: 17 residues processed: 131 average time/residue: 0.1051 time to fit residues: 18.1843 Evaluate side-chains 131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 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 = 0.3987 r_free = 0.3987 target = 0.177471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134829 restraints weight = 8373.932| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.83 r_work: 0.3330 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7881 Z= 0.114 Angle : 0.496 7.662 10693 Z= 0.255 Chirality : 0.041 0.154 1259 Planarity : 0.004 0.050 1362 Dihedral : 3.697 17.323 1061 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.34 % Allowed : 17.56 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.27), residues: 997 helix: 1.21 (0.24), residues: 512 sheet: -1.13 (0.45), residues: 107 loop : -0.40 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 666 TYR 0.016 0.002 TYR A 586 PHE 0.024 0.001 PHE A 759 TRP 0.011 0.001 TRP A 927 HIS 0.002 0.000 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7880) covalent geometry : angle 0.49564 (10693) hydrogen bonds : bond 0.03697 ( 415) hydrogen bonds : angle 3.96177 ( 1269) Misc. bond : bond 0.00071 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.70 seconds wall clock time: 42 minutes 12.79 seconds (2532.79 seconds total)