Starting phenix.real_space_refine on Tue Mar 3 18:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln6_0925/03_2026/6ln6_0925.cif" } resolution = 2.9 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= 0.013 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 Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4986 2.51 5 N 1310 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 7836 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7802 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 46, 'TRANS': 963} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.60, per 1000 atoms: 0.20 Number of scatterers: 7836 At special positions: 0 Unit cell: (103.335, 79.68, 140.685, 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) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1477 8.00 N 1310 7.00 C 4986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.02 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: 0.83 Conformation dependent library (CDL) restraints added in 294.9 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 53.3% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.740A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 120 removed outlier: 3.913A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (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 230 removed outlier: 3.695A pdb=" N THR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.543A pdb=" N ASN A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.826A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 281 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.876A pdb=" N THR A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.686A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 468 Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.501A pdb=" N SER A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.615A pdb=" N ARG A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.623A pdb=" N LYS A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.553A pdb=" N ASN A 582 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 4.307A pdb=" N ALA A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.593A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.648A 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 713 Processing helix chain 'A' and resid 723 through 729 removed outlier: 3.506A pdb=" N ALA A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 781 removed outlier: 3.853A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 removed outlier: 3.557A pdb=" N ASN A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 814 through 818 removed outlier: 4.128A pdb=" N LYS A 818 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 857 removed outlier: 3.546A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 Processing helix chain 'A' and resid 888 through 891 removed outlier: 3.507A pdb=" N GLU A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 892 through 912 removed outlier: 4.445A 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 950 through 957 removed outlier: 4.631A pdb=" N LEU A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.730A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 removed outlier: 3.529A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.677A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.916A 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 188 removed outlier: 3.538A pdb=" N ALA A 216 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.511A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 348 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 623 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER A 350 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.780A pdb=" N VAL A 395 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.238A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.730A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.780A pdb=" N VAL A 395 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.948A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.554A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 15.050A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 4.780A pdb=" N VAL A 395 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.948A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.554A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 15.050A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.490A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU A 590 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A 594 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428 438 hydrogen bonds defined for protein. 1257 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: 1.33 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2572 1.35 - 1.48: 1792 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7981 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.616 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.299 0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 7976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 10786 3.23 - 6.45: 45 6.45 - 9.68: 3 9.68 - 12.90: 4 12.90 - 16.13: 1 Bond angle restraints: 10839 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.88 -16.13 3.00e+00 1.11e-01 2.89e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.22 -12.17 3.00e+00 1.11e-01 1.64e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.30 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 108.87 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 109.05 9.90 3.00e+00 1.11e-01 1.09e+01 ... (remaining 10834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 4698 25.54 - 51.08: 144 51.08 - 76.62: 14 76.62 - 102.16: 3 102.16 - 127.70: 1 Dihedral angle restraints: 4860 sinusoidal: 1941 harmonic: 2919 Sorted by residual: dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 78.95 -127.70 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN A 421 " pdb=" C ASN A 421 " pdb=" N ASP A 422 " pdb=" CA ASP A 422 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1177 0.076 - 0.151: 95 0.151 - 0.227: 0 0.227 - 0.303: 0 0.303 - 0.378: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO A 248 " pdb=" N PRO A 248 " pdb=" C PRO A 248 " pdb=" CB PRO A 248 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL A 194 " pdb=" N VAL A 194 " pdb=" C VAL A 194 " pdb=" CB VAL A 194 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1270 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1017 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 502 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO A 503 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 975 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 83 2.61 - 3.18: 6646 3.18 - 3.75: 11998 3.75 - 4.33: 17790 4.33 - 4.90: 28873 Nonbonded interactions: 65390 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.035 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.125 2.170 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 351 " pdb="MG MG A2002 " model vdw 2.191 2.170 ... (remaining 65385 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.670 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: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.005 0.226 7982 Z= 0.260 Angle : 0.642 16.126 10841 Z= 0.341 Chirality : 0.041 0.378 1273 Planarity : 0.004 0.045 1376 Dihedral : 12.490 127.700 2965 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -3.94 (0.20), residues: 1006 helix: -3.34 (0.14), residues: 484 sheet: -1.64 (0.37), residues: 124 loop : -1.65 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.006 0.001 TYR A 842 PHE 0.011 0.001 PHE A 367 TRP 0.007 0.001 TRP A 793 HIS 0.007 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 7981) covalent geometry : angle 0.64214 (10839) SS BOND : bond 0.00844 ( 1) SS BOND : angle 0.49379 ( 2) hydrogen bonds : bond 0.24670 ( 399) hydrogen bonds : angle 8.97642 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8025 (mttp) cc_final: 0.7803 (mtmt) REVERT: A 33 LYS cc_start: 0.8070 (tttt) cc_final: 0.7564 (ttpt) REVERT: A 83 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6276 (mp0) REVERT: A 135 LYS cc_start: 0.8128 (mppt) cc_final: 0.7712 (tptt) REVERT: A 172 THR cc_start: 0.8481 (m) cc_final: 0.8266 (t) REVERT: A 179 ILE cc_start: 0.7648 (mp) cc_final: 0.7404 (tt) REVERT: A 231 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 235 ILE cc_start: 0.7476 (pt) cc_final: 0.7203 (pp) REVERT: A 290 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7083 (mtp85) REVERT: A 297 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7733 (mttt) REVERT: A 494 MET cc_start: 0.8607 (ttt) cc_final: 0.7832 (tmm) REVERT: A 542 GLN cc_start: 0.7434 (mp10) cc_final: 0.7079 (mp-120) REVERT: A 575 MET cc_start: 0.7900 (mtt) cc_final: 0.7681 (mtm) REVERT: A 615 GLN cc_start: 0.7812 (tt0) cc_final: 0.7236 (mt0) REVERT: A 693 PHE cc_start: 0.8075 (m-10) cc_final: 0.7667 (m-10) REVERT: A 883 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6832 (mm-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.5336 time to fit residues: 98.8248 Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS A 19 ASN A 190 HIS A 421 ASN A 453 ASN A 501 ASN A 568 ASN A 582 ASN A 817 ASN A 868 GLN A 913 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.148586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115993 restraints weight = 8393.694| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.60 r_work: 0.3060 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7982 Z= 0.113 Angle : 0.522 5.557 10841 Z= 0.274 Chirality : 0.042 0.132 1273 Planarity : 0.005 0.050 1376 Dihedral : 8.064 148.367 1102 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.50 % Allowed : 10.53 % Favored : 87.96 % 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: -1.16 (0.24), residues: 1006 helix: -0.38 (0.22), residues: 492 sheet: -1.26 (0.42), residues: 124 loop : -0.90 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 371 TYR 0.010 0.001 TYR A 497 PHE 0.015 0.001 PHE A 367 TRP 0.012 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7981) covalent geometry : angle 0.52185 (10839) SS BOND : bond 0.00677 ( 1) SS BOND : angle 0.79028 ( 2) hydrogen bonds : bond 0.04393 ( 399) hydrogen bonds : angle 4.62915 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.240 Fit side-chains REVERT: A 33 LYS cc_start: 0.8117 (tttt) cc_final: 0.7612 (ttpt) REVERT: A 83 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6045 (mp0) REVERT: A 135 LYS cc_start: 0.8504 (mppt) cc_final: 0.7813 (tptt) REVERT: A 179 ILE cc_start: 0.7652 (mp) cc_final: 0.7354 (tt) REVERT: A 231 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 235 ILE cc_start: 0.7484 (pt) cc_final: 0.7084 (pp) REVERT: A 290 ARG cc_start: 0.7345 (tpp80) cc_final: 0.6861 (mtp85) REVERT: A 297 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8237 (mtpp) REVERT: A 494 MET cc_start: 0.8882 (ttt) cc_final: 0.8135 (tmm) REVERT: A 615 GLN cc_start: 0.8273 (tt0) cc_final: 0.7469 (mt0) REVERT: A 689 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: A 816 MET cc_start: 0.8484 (mmm) cc_final: 0.8244 (mmm) REVERT: A 883 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6722 (mm-30) REVERT: A 981 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7877 (mm-30) outliers start: 13 outliers final: 4 residues processed: 139 average time/residue: 0.5372 time to fit residues: 79.2584 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 88 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 403 ASN A 568 ASN A 582 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116248 restraints weight = 8230.485| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.61 r_work: 0.3035 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7982 Z= 0.105 Angle : 0.486 5.890 10841 Z= 0.252 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.048 1376 Dihedral : 8.013 150.673 1102 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.39 % Allowed : 12.50 % Favored : 86.11 % 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: -0.04 (0.26), residues: 1006 helix: 0.80 (0.24), residues: 496 sheet: -1.00 (0.44), residues: 124 loop : -0.65 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 371 TYR 0.010 0.001 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.011 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7981) covalent geometry : angle 0.48597 (10839) SS BOND : bond 0.00331 ( 1) SS BOND : angle 0.70731 ( 2) hydrogen bonds : bond 0.03751 ( 399) hydrogen bonds : angle 4.18751 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.292 Fit side-chains REVERT: A 33 LYS cc_start: 0.8043 (tttt) cc_final: 0.7559 (ttpt) REVERT: A 135 LYS cc_start: 0.8534 (mppt) cc_final: 0.7833 (tptt) REVERT: A 179 ILE cc_start: 0.7728 (mp) cc_final: 0.7461 (tt) REVERT: A 231 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 235 ILE cc_start: 0.7402 (pt) cc_final: 0.6988 (pp) REVERT: A 290 ARG cc_start: 0.7177 (tpp80) cc_final: 0.6604 (mtp85) REVERT: A 433 VAL cc_start: 0.8127 (m) cc_final: 0.7878 (p) REVERT: A 494 MET cc_start: 0.8897 (ttt) cc_final: 0.8173 (tmm) REVERT: A 615 GLN cc_start: 0.8377 (tt0) cc_final: 0.7567 (mt0) REVERT: A 689 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: A 816 MET cc_start: 0.8494 (mmm) cc_final: 0.8172 (mmm) REVERT: A 883 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6642 (mm-30) REVERT: A 1023 MET cc_start: 0.6100 (tpt) cc_final: 0.5781 (tpp) outliers start: 12 outliers final: 6 residues processed: 135 average time/residue: 0.5364 time to fit residues: 76.8804 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113378 restraints weight = 8366.539| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.62 r_work: 0.2978 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7982 Z= 0.147 Angle : 0.533 7.444 10841 Z= 0.273 Chirality : 0.043 0.133 1273 Planarity : 0.005 0.047 1376 Dihedral : 8.341 156.942 1102 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 13.66 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.21 (0.26), residues: 1006 helix: 1.06 (0.24), residues: 490 sheet: -0.79 (0.43), residues: 129 loop : -0.61 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 371 TYR 0.011 0.001 TYR A 295 PHE 0.018 0.001 PHE A 367 TRP 0.009 0.001 TRP A 854 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7981) covalent geometry : angle 0.53255 (10839) SS BOND : bond 0.00862 ( 1) SS BOND : angle 0.75303 ( 2) hydrogen bonds : bond 0.04048 ( 399) hydrogen bonds : angle 4.28743 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.267 Fit side-chains REVERT: A 33 LYS cc_start: 0.8090 (tttt) cc_final: 0.7588 (ttpt) REVERT: A 133 ASP cc_start: 0.7382 (p0) cc_final: 0.7173 (p0) REVERT: A 139 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7903 (mtp85) REVERT: A 179 ILE cc_start: 0.7641 (mp) cc_final: 0.7372 (tt) REVERT: A 231 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8295 (mm-30) REVERT: A 235 ILE cc_start: 0.7549 (pt) cc_final: 0.7125 (pp) REVERT: A 290 ARG cc_start: 0.7318 (tpp80) cc_final: 0.6739 (mtp85) REVERT: A 494 MET cc_start: 0.8957 (ttt) cc_final: 0.8328 (tmm) REVERT: A 542 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: A 615 GLN cc_start: 0.8405 (tt0) cc_final: 0.7590 (mt0) REVERT: A 689 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: A 816 MET cc_start: 0.8581 (mmm) cc_final: 0.8239 (mmm) REVERT: A 883 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 1023 MET cc_start: 0.6333 (tpt) cc_final: 0.6026 (tpp) outliers start: 17 outliers final: 7 residues processed: 135 average time/residue: 0.5552 time to fit residues: 79.2898 Evaluate side-chains 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110339 restraints weight = 8385.596| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.62 r_work: 0.2956 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7982 Z= 0.184 Angle : 0.572 8.218 10841 Z= 0.293 Chirality : 0.045 0.139 1273 Planarity : 0.005 0.051 1376 Dihedral : 8.523 159.500 1102 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.78 % Allowed : 14.24 % Favored : 82.99 % 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: 0.18 (0.26), residues: 1006 helix: 1.01 (0.24), residues: 488 sheet: -0.92 (0.44), residues: 109 loop : -0.58 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 371 TYR 0.013 0.002 TYR A 295 PHE 0.021 0.001 PHE A 367 TRP 0.012 0.001 TRP A 107 HIS 0.006 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 7981) covalent geometry : angle 0.57190 (10839) SS BOND : bond 0.00925 ( 1) SS BOND : angle 1.04896 ( 2) hydrogen bonds : bond 0.04409 ( 399) hydrogen bonds : angle 4.39873 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.316 Fit side-chains REVERT: A 33 LYS cc_start: 0.8122 (tttt) cc_final: 0.7586 (ttpt) REVERT: A 58 GLU cc_start: 0.7790 (pp20) cc_final: 0.7547 (pp20) REVERT: A 139 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7716 (mtp85) REVERT: A 153 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7581 (tp) REVERT: A 179 ILE cc_start: 0.7724 (mp) cc_final: 0.7386 (tt) REVERT: A 203 ASP cc_start: 0.7609 (t0) cc_final: 0.7405 (t0) REVERT: A 231 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 235 ILE cc_start: 0.7515 (pt) cc_final: 0.7066 (pp) REVERT: A 290 ARG cc_start: 0.7388 (tpp80) cc_final: 0.6836 (mtp85) REVERT: A 494 MET cc_start: 0.8950 (ttt) cc_final: 0.8294 (tmm) REVERT: A 615 GLN cc_start: 0.8400 (tt0) cc_final: 0.7591 (mt0) REVERT: A 689 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: A 816 MET cc_start: 0.8543 (mmm) cc_final: 0.8265 (mmm) REVERT: A 883 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 1023 MET cc_start: 0.6432 (tpt) cc_final: 0.6080 (tpp) outliers start: 24 outliers final: 11 residues processed: 137 average time/residue: 0.5495 time to fit residues: 79.9913 Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 763 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.111047 restraints weight = 8348.973| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.63 r_work: 0.2968 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7982 Z= 0.157 Angle : 0.543 7.784 10841 Z= 0.279 Chirality : 0.044 0.132 1273 Planarity : 0.005 0.055 1376 Dihedral : 8.484 159.189 1102 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.43 % Allowed : 14.70 % Favored : 82.87 % 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 (0.26), residues: 1006 helix: 1.09 (0.24), residues: 490 sheet: -0.87 (0.45), residues: 109 loop : -0.54 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 371 TYR 0.011 0.001 TYR A 295 PHE 0.019 0.001 PHE A 367 TRP 0.012 0.001 TRP A 793 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 7981) covalent geometry : angle 0.54273 (10839) SS BOND : bond 0.00837 ( 1) SS BOND : angle 1.03088 ( 2) hydrogen bonds : bond 0.04099 ( 399) hydrogen bonds : angle 4.27282 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.294 Fit side-chains REVERT: A 33 LYS cc_start: 0.8084 (tttt) cc_final: 0.7540 (ttpt) REVERT: A 58 GLU cc_start: 0.7916 (pp20) cc_final: 0.7686 (pp20) REVERT: A 179 ILE cc_start: 0.7681 (mp) cc_final: 0.7372 (tt) REVERT: A 203 ASP cc_start: 0.7559 (t0) cc_final: 0.7357 (t0) REVERT: A 231 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 235 ILE cc_start: 0.7524 (pt) cc_final: 0.7103 (pp) REVERT: A 290 ARG cc_start: 0.7428 (tpp80) cc_final: 0.6886 (mtp85) REVERT: A 435 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: A 494 MET cc_start: 0.8947 (ttt) cc_final: 0.8269 (tmm) REVERT: A 542 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: A 615 GLN cc_start: 0.8363 (tt0) cc_final: 0.7559 (mt0) REVERT: A 689 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 816 MET cc_start: 0.8546 (mmm) cc_final: 0.8242 (mmm) REVERT: A 883 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6925 (mm-30) REVERT: A 1023 MET cc_start: 0.6536 (tpt) cc_final: 0.6217 (tpp) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.5590 time to fit residues: 78.2107 Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Chi-restraints excluded: chain A residue 715 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 568 ASN A 582 ASN A 758 GLN A 874 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121356 restraints weight = 8227.990| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.52 r_work: 0.3032 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7982 Z= 0.103 Angle : 0.480 6.127 10841 Z= 0.248 Chirality : 0.041 0.126 1273 Planarity : 0.004 0.055 1376 Dihedral : 8.249 156.178 1102 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.85 % Allowed : 15.51 % Favored : 82.64 % 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: 0.72 (0.27), residues: 1006 helix: 1.48 (0.24), residues: 490 sheet: -0.71 (0.44), residues: 130 loop : -0.30 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 371 TYR 0.011 0.001 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.013 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7981) covalent geometry : angle 0.48007 (10839) SS BOND : bond 0.00630 ( 1) SS BOND : angle 0.75868 ( 2) hydrogen bonds : bond 0.03399 ( 399) hydrogen bonds : angle 3.99692 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.268 Fit side-chains REVERT: A 27 GLU cc_start: 0.6719 (mp0) cc_final: 0.6462 (pt0) REVERT: A 33 LYS cc_start: 0.8025 (tttt) cc_final: 0.7523 (ttpt) REVERT: A 58 GLU cc_start: 0.7812 (pp20) cc_final: 0.7579 (pp20) REVERT: A 153 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 179 ILE cc_start: 0.7681 (mp) cc_final: 0.7438 (tt) REVERT: A 180 LEU cc_start: 0.8535 (tp) cc_final: 0.8244 (tt) REVERT: A 231 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8250 (mm-30) REVERT: A 235 ILE cc_start: 0.7519 (pt) cc_final: 0.7066 (pp) REVERT: A 290 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6801 (mtp85) REVERT: A 339 VAL cc_start: 0.7934 (p) cc_final: 0.7568 (t) REVERT: A 494 MET cc_start: 0.8889 (ttt) cc_final: 0.8217 (tmm) REVERT: A 542 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: A 615 GLN cc_start: 0.8367 (tt0) cc_final: 0.7584 (mt0) REVERT: A 689 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: A 816 MET cc_start: 0.8563 (mmm) cc_final: 0.8249 (mmm) REVERT: A 883 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6825 (mm-30) REVERT: A 1023 MET cc_start: 0.6230 (tpt) cc_final: 0.6015 (mmm) outliers start: 16 outliers final: 9 residues processed: 134 average time/residue: 0.5480 time to fit residues: 77.9519 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113553 restraints weight = 8352.295| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.64 r_work: 0.2998 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7982 Z= 0.111 Angle : 0.494 6.603 10841 Z= 0.254 Chirality : 0.042 0.127 1273 Planarity : 0.005 0.057 1376 Dihedral : 8.262 155.813 1102 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.62 % Allowed : 16.09 % Favored : 82.29 % 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: 0.83 (0.27), residues: 1006 helix: 1.57 (0.24), residues: 491 sheet: -0.68 (0.43), residues: 135 loop : -0.22 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 371 TYR 0.011 0.001 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.011 0.001 TRP A 854 HIS 0.003 0.000 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7981) covalent geometry : angle 0.49390 (10839) SS BOND : bond 0.00853 ( 1) SS BOND : angle 0.93309 ( 2) hydrogen bonds : bond 0.03493 ( 399) hydrogen bonds : angle 3.97965 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.240 Fit side-chains REVERT: A 27 GLU cc_start: 0.6764 (mp0) cc_final: 0.6490 (pt0) REVERT: A 33 LYS cc_start: 0.8021 (tttt) cc_final: 0.7511 (ttpt) REVERT: A 153 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7455 (tp) REVERT: A 179 ILE cc_start: 0.7652 (mp) cc_final: 0.7413 (tt) REVERT: A 180 LEU cc_start: 0.8556 (tp) cc_final: 0.8225 (tt) REVERT: A 231 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8267 (mm-30) REVERT: A 235 ILE cc_start: 0.7472 (pt) cc_final: 0.7006 (pp) REVERT: A 290 ARG cc_start: 0.7305 (tpp80) cc_final: 0.6770 (mtp85) REVERT: A 339 VAL cc_start: 0.7877 (p) cc_final: 0.7526 (t) REVERT: A 494 MET cc_start: 0.8913 (ttt) cc_final: 0.8262 (tmm) REVERT: A 615 GLN cc_start: 0.8389 (tt0) cc_final: 0.7594 (mt0) REVERT: A 658 ASP cc_start: 0.7265 (m-30) cc_final: 0.6979 (m-30) REVERT: A 689 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: A 816 MET cc_start: 0.8579 (mmm) cc_final: 0.8231 (mmm) REVERT: A 883 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6805 (mm-30) REVERT: A 1023 MET cc_start: 0.6037 (tpt) cc_final: 0.5831 (mmm) outliers start: 14 outliers final: 8 residues processed: 128 average time/residue: 0.5867 time to fit residues: 79.4924 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115010 restraints weight = 8272.345| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.62 r_work: 0.3071 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7982 Z= 0.131 Angle : 0.518 6.989 10841 Z= 0.267 Chirality : 0.042 0.128 1273 Planarity : 0.005 0.058 1376 Dihedral : 8.336 156.488 1102 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.62 % Allowed : 16.55 % Favored : 81.83 % 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: 0.74 (0.26), residues: 1006 helix: 1.48 (0.24), residues: 491 sheet: -0.71 (0.43), residues: 135 loop : -0.24 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 371 TYR 0.011 0.001 TYR A 842 PHE 0.016 0.001 PHE A 367 TRP 0.010 0.001 TRP A 854 HIS 0.004 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7981) covalent geometry : angle 0.51827 (10839) SS BOND : bond 0.00809 ( 1) SS BOND : angle 0.89069 ( 2) hydrogen bonds : bond 0.03720 ( 399) hydrogen bonds : angle 4.04854 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.306 Fit side-chains REVERT: A 33 LYS cc_start: 0.8002 (tttt) cc_final: 0.7510 (ttpt) REVERT: A 153 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7495 (tp) REVERT: A 179 ILE cc_start: 0.7865 (mp) cc_final: 0.7591 (tt) REVERT: A 231 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 235 ILE cc_start: 0.7524 (pt) cc_final: 0.7076 (pp) REVERT: A 290 ARG cc_start: 0.7292 (tpp80) cc_final: 0.6707 (mtp85) REVERT: A 339 VAL cc_start: 0.8007 (p) cc_final: 0.7588 (t) REVERT: A 453 ASN cc_start: 0.8636 (t0) cc_final: 0.8293 (t0) REVERT: A 494 MET cc_start: 0.8896 (ttt) cc_final: 0.8264 (tmm) REVERT: A 615 GLN cc_start: 0.8384 (tt0) cc_final: 0.7587 (mt0) REVERT: A 689 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: A 816 MET cc_start: 0.8538 (mmm) cc_final: 0.8172 (mmm) REVERT: A 883 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6800 (mm-30) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.5692 time to fit residues: 75.4748 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.110062 restraints weight = 8362.773| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.66 r_work: 0.2981 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7982 Z= 0.164 Angle : 0.558 7.781 10841 Z= 0.287 Chirality : 0.044 0.133 1273 Planarity : 0.005 0.057 1376 Dihedral : 8.474 158.589 1102 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.74 % Allowed : 16.44 % Favored : 81.83 % 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: 0.55 (0.26), residues: 1006 helix: 1.31 (0.24), residues: 490 sheet: -0.85 (0.44), residues: 115 loop : -0.34 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 371 TYR 0.012 0.002 TYR A 295 PHE 0.018 0.001 PHE A 367 TRP 0.009 0.001 TRP A 107 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 7981) covalent geometry : angle 0.55777 (10839) SS BOND : bond 0.00939 ( 1) SS BOND : angle 0.97717 ( 2) hydrogen bonds : bond 0.04125 ( 399) hydrogen bonds : angle 4.18896 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.298 Fit side-chains REVERT: A 27 GLU cc_start: 0.6843 (mp0) cc_final: 0.6550 (pt0) REVERT: A 33 LYS cc_start: 0.8044 (tttt) cc_final: 0.7521 (ttpt) REVERT: A 153 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 179 ILE cc_start: 0.7921 (mp) cc_final: 0.7579 (tt) REVERT: A 231 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 235 ILE cc_start: 0.7535 (pt) cc_final: 0.7116 (pp) REVERT: A 290 ARG cc_start: 0.7469 (tpp80) cc_final: 0.6914 (mtp85) REVERT: A 453 ASN cc_start: 0.8624 (t0) cc_final: 0.8368 (t0) REVERT: A 494 MET cc_start: 0.8948 (ttt) cc_final: 0.8274 (tmm) REVERT: A 615 GLN cc_start: 0.8402 (tt0) cc_final: 0.7600 (mt0) REVERT: A 689 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: A 816 MET cc_start: 0.8570 (mmm) cc_final: 0.8235 (mmm) REVERT: A 883 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6998 (mm-30) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.5810 time to fit residues: 77.3499 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 689 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN A 582 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115134 restraints weight = 8323.207| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.66 r_work: 0.3088 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7982 Z= 0.095 Angle : 0.482 5.935 10841 Z= 0.250 Chirality : 0.041 0.125 1273 Planarity : 0.005 0.058 1376 Dihedral : 8.159 154.188 1102 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.27 % Allowed : 17.13 % Favored : 81.60 % 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: 1.01 (0.27), residues: 1006 helix: 1.72 (0.24), residues: 491 sheet: -0.58 (0.43), residues: 133 loop : -0.15 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 371 TYR 0.011 0.001 TYR A 842 PHE 0.013 0.001 PHE A 367 TRP 0.014 0.001 TRP A 793 HIS 0.002 0.000 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 7981) covalent geometry : angle 0.48157 (10839) SS BOND : bond 0.00605 ( 1) SS BOND : angle 0.88559 ( 2) hydrogen bonds : bond 0.03215 ( 399) hydrogen bonds : angle 3.89174 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.64 seconds wall clock time: 50 minutes 11.47 seconds (3011.47 seconds total)