Starting phenix.real_space_refine on Tue Mar 3 17:47:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2026/7wge_32484.map" } resolution = 3.4 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1495 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4099 2.51 5 N 1121 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 6460 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 5630 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 828 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.42, per 1000 atoms: 0.37 Number of scatterers: 6460 At special positions: 0 Unit cell: (68.475, 92.13, 140.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1189 8.00 N 1121 7.00 C 4099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 35 " distance=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 430.4 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 49.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 299 through 307 removed outlier: 3.633A pdb=" N TYR A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.645A pdb=" N LEU A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 368 through 375 removed outlier: 4.014A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.589A pdb=" N ILE A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 435 through 445 removed outlier: 3.663A pdb=" N GLY A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 510 through 517 Processing helix chain 'A' and resid 519 through 536 removed outlier: 4.728A pdb=" N ARG A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 559 Processing helix chain 'A' and resid 565 through 581 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.658A pdb=" N LEU A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 592 " --> pdb=" O PRO A 588 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 594' Processing helix chain 'A' and resid 597 through 608 Processing helix chain 'A' and resid 623 through 640 removed outlier: 3.558A pdb=" N SER A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.648A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 690 removed outlier: 4.165A pdb=" N GLU A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET A 686 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLU A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 Processing helix chain 'A' and resid 702 through 710 removed outlier: 4.308A pdb=" N SER A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 747 through 760 Processing helix chain 'A' and resid 795 through 801 Processing helix chain 'A' and resid 821 through 834 Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.718A pdb=" N LYS A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 removed outlier: 3.563A pdb=" N LEU A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 888 " --> pdb=" O HIS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 910 through 921 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 964 through 978 removed outlier: 3.821A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 removed outlier: 4.105A pdb=" N GLY B 19 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 49 removed outlier: 3.804A pdb=" N LYS B 36 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 94 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 366 removed outlier: 6.798A pdb=" N HIS A 363 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE A 408 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 365 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 405 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 455 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE A 407 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 457 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 428 Processing sheet with id=AA3, first strand: chain 'A' and resid 585 through 586 removed outlier: 3.978A pdb=" N SER A 620 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 744 removed outlier: 3.606A pdb=" N PHE A 787 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS A 766 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU A 786 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN A 768 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU A 767 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 843 " --> pdb=" O LEU A 813 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.961A pdb=" N ILE B 3 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ASP B 59 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B 5 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 22 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU B 56 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 24 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 58 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ASP B 26 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 77 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE B 78 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU B 89 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N PHE B 80 " --> pdb=" O ILE B 87 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 725 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: 1.21 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 2183 1.37 - 1.52: 1846 1.52 - 1.66: 2499 1.66 - 1.80: 41 1.80 - 1.95: 24 Bond restraints: 6593 Sorted by residual: bond pdb=" CA GLY A 309 " pdb=" C GLY A 309 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.48e+00 bond pdb=" N GLY A 309 " pdb=" CA GLY A 309 " ideal model delta sigma weight residual 1.449 1.466 -0.017 1.45e-02 4.76e+03 1.34e+00 bond pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.51e-01 bond pdb=" CA ASP A 935 " pdb=" CB ASP A 935 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.60e-01 bond pdb=" CB PRO A 320 " pdb=" CG PRO A 320 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.33e-01 ... (remaining 6588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 8637 1.48 - 2.96: 228 2.96 - 4.44: 48 4.44 - 5.92: 15 5.92 - 7.40: 6 Bond angle restraints: 8934 Sorted by residual: angle pdb=" N MET A 741 " pdb=" CA MET A 741 " pdb=" C MET A 741 " ideal model delta sigma weight residual 114.56 109.17 5.39 1.27e+00 6.20e-01 1.80e+01 angle pdb=" C LEU A 934 " pdb=" N ASP A 935 " pdb=" CA ASP A 935 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 angle pdb=" CA MET A 741 " pdb=" C MET A 741 " pdb=" N GLY A 742 " ideal model delta sigma weight residual 119.26 116.19 3.07 1.14e+00 7.69e-01 7.27e+00 angle pdb=" N HIS A 737 " pdb=" CA HIS A 737 " pdb=" C HIS A 737 " ideal model delta sigma weight residual 113.19 108.94 4.25 1.58e+00 4.01e-01 7.24e+00 angle pdb=" CG ARG A 773 " pdb=" CD ARG A 773 " pdb=" NE ARG A 773 " ideal model delta sigma weight residual 112.00 117.23 -5.23 2.20e+00 2.07e-01 5.64e+00 ... (remaining 8929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3627 17.92 - 35.85: 330 35.85 - 53.77: 68 53.77 - 71.69: 21 71.69 - 89.61: 8 Dihedral angle restraints: 4054 sinusoidal: 1680 harmonic: 2374 Sorted by residual: dihedral pdb=" CA PRO A 616 " pdb=" C PRO A 616 " pdb=" N LEU A 617 " pdb=" CA LEU A 617 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP A 387 " pdb=" CB ASP A 387 " pdb=" CG ASP A 387 " pdb=" OD1 ASP A 387 " ideal model delta sinusoidal sigma weight residual -30.00 -86.71 56.71 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA LYS B 36 " pdb=" C LYS B 36 " pdb=" N MET B 37 " pdb=" CA MET B 37 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 ... (remaining 4051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 782 0.043 - 0.085: 183 0.085 - 0.128: 53 0.128 - 0.170: 2 0.170 - 0.213: 3 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CB VAL A 296 " pdb=" CA VAL A 296 " pdb=" CG1 VAL A 296 " pdb=" CG2 VAL A 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU A 934 " pdb=" CB LEU A 934 " pdb=" CD1 LEU A 934 " pdb=" CD2 LEU A 934 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 615 " pdb=" N ILE A 615 " pdb=" C ILE A 615 " pdb=" CB ILE A 615 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1020 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 319 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO A 320 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 565 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 566 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 712 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO A 713 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " 0.024 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 277 2.73 - 3.27: 6621 3.27 - 3.81: 10282 3.81 - 4.36: 12321 4.36 - 4.90: 21031 Nonbonded interactions: 50532 Sorted by model distance: nonbonded pdb=" OG SER A 587 " pdb=" OD1 ASP A 589 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU A 812 " pdb=" OG1 THR A 841 " model vdw 2.243 3.040 nonbonded pdb=" O ILE A 662 " pdb=" ND1 HIS A 663 " model vdw 2.248 3.120 nonbonded pdb=" OG SER A 341 " pdb="MG MG A1002 " model vdw 2.259 2.170 nonbonded pdb=" OE2 GLU A 683 " pdb=" ND2 ASN A 699 " model vdw 2.278 3.120 ... (remaining 50527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 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 : 0.003 0.046 6594 Z= 0.120 Angle : 0.631 7.401 8936 Z= 0.315 Chirality : 0.040 0.213 1023 Planarity : 0.005 0.078 1133 Dihedral : 15.024 89.613 2509 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.43 (0.30), residues: 807 helix: 1.54 (0.28), residues: 344 sheet: -0.37 (0.52), residues: 111 loop : -2.23 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 773 TYR 0.007 0.001 TYR A 723 PHE 0.011 0.001 PHE A 454 TRP 0.027 0.002 TRP A 351 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6593) covalent geometry : angle 0.63074 ( 8934) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.59911 ( 2) hydrogen bonds : bond 0.16232 ( 252) hydrogen bonds : angle 5.77633 ( 725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0892 time to fit residues: 16.3424 Evaluate side-chains 96 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.215631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.192983 restraints weight = 26433.368| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 4.34 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6594 Z= 0.165 Angle : 0.732 13.823 8936 Z= 0.361 Chirality : 0.044 0.217 1023 Planarity : 0.005 0.059 1133 Dihedral : 6.334 54.841 902 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 1.81 % Allowed : 10.00 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.64 (0.30), residues: 807 helix: 1.05 (0.27), residues: 365 sheet: -0.41 (0.50), residues: 112 loop : -2.19 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 773 TYR 0.014 0.002 TYR A 796 PHE 0.044 0.002 PHE A 673 TRP 0.020 0.002 TRP A 703 HIS 0.004 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6593) covalent geometry : angle 0.73192 ( 8934) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.41332 ( 2) hydrogen bonds : bond 0.04253 ( 252) hydrogen bonds : angle 4.81265 ( 725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.256 Fit side-chains REVERT: A 313 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6788 (tt0) outliers start: 11 outliers final: 7 residues processed: 106 average time/residue: 0.0930 time to fit residues: 13.0335 Evaluate side-chains 95 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.208811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.186939 restraints weight = 26328.430| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 4.06 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4138 r_free = 0.4138 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4137 r_free = 0.4137 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.142 Angle : 0.641 12.327 8936 Z= 0.319 Chirality : 0.042 0.211 1023 Planarity : 0.005 0.052 1133 Dihedral : 6.414 62.935 902 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 1.94 % Allowed : 11.81 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.63 (0.30), residues: 807 helix: 1.09 (0.27), residues: 373 sheet: -0.31 (0.51), residues: 110 loop : -2.32 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 773 TYR 0.021 0.002 TYR A 489 PHE 0.029 0.002 PHE A 738 TRP 0.035 0.002 TRP A 789 HIS 0.003 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6593) covalent geometry : angle 0.64139 ( 8934) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.32445 ( 2) hydrogen bonds : bond 0.03999 ( 252) hydrogen bonds : angle 4.54910 ( 725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.248 Fit side-chains REVERT: A 313 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: A 799 ILE cc_start: 0.8312 (tp) cc_final: 0.8005 (tp) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.1020 time to fit residues: 14.5209 Evaluate side-chains 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.205836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.181376 restraints weight = 27931.982| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 4.76 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6594 Z= 0.123 Angle : 0.646 13.789 8936 Z= 0.315 Chirality : 0.041 0.228 1023 Planarity : 0.005 0.053 1133 Dihedral : 6.223 60.872 902 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.36 % Allowed : 13.33 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.57 (0.30), residues: 807 helix: 1.25 (0.27), residues: 373 sheet: -0.46 (0.50), residues: 115 loop : -2.41 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 836 TYR 0.019 0.002 TYR A 493 PHE 0.031 0.002 PHE A 738 TRP 0.028 0.001 TRP A 789 HIS 0.003 0.001 HIS A 663 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6593) covalent geometry : angle 0.64564 ( 8934) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.40508 ( 2) hydrogen bonds : bond 0.03464 ( 252) hydrogen bonds : angle 4.38440 ( 725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.258 Fit side-chains REVERT: A 313 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: A 534 MET cc_start: 0.7719 (ptp) cc_final: 0.7477 (ptp) REVERT: A 680 ASP cc_start: 0.7892 (m-30) cc_final: 0.7652 (m-30) REVERT: A 717 GLU cc_start: 0.6551 (pm20) cc_final: 0.6191 (mt-10) REVERT: A 771 GLU cc_start: 0.7860 (tp30) cc_final: 0.7215 (tp30) REVERT: A 799 ILE cc_start: 0.8329 (tp) cc_final: 0.7931 (tp) REVERT: B 49 MET cc_start: 0.4643 (ptp) cc_final: 0.4391 (ptp) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.0852 time to fit residues: 12.6278 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.202793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.178454 restraints weight = 29122.545| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 4.63 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6594 Z= 0.129 Angle : 0.647 12.884 8936 Z= 0.317 Chirality : 0.041 0.203 1023 Planarity : 0.004 0.053 1133 Dihedral : 6.138 59.373 902 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.22 % Allowed : 14.17 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.30), residues: 807 helix: 1.20 (0.27), residues: 383 sheet: -0.18 (0.54), residues: 105 loop : -2.48 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 99 TYR 0.015 0.002 TYR A 796 PHE 0.028 0.001 PHE A 738 TRP 0.024 0.001 TRP A 789 HIS 0.007 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6593) covalent geometry : angle 0.64690 ( 8934) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.33968 ( 2) hydrogen bonds : bond 0.03396 ( 252) hydrogen bonds : angle 4.33814 ( 725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.271 Fit side-chains REVERT: A 313 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: A 534 MET cc_start: 0.7778 (ptp) cc_final: 0.7477 (ptp) REVERT: A 680 ASP cc_start: 0.8038 (m-30) cc_final: 0.7790 (m-30) REVERT: A 771 GLU cc_start: 0.7977 (tp30) cc_final: 0.7258 (tp30) REVERT: B 49 MET cc_start: 0.4714 (ptp) cc_final: 0.4388 (ptp) outliers start: 14 outliers final: 8 residues processed: 112 average time/residue: 0.0940 time to fit residues: 13.7839 Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.197610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.166327 restraints weight = 35291.172| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 7.14 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6594 Z= 0.169 Angle : 0.708 14.934 8936 Z= 0.346 Chirality : 0.042 0.215 1023 Planarity : 0.005 0.052 1133 Dihedral : 6.466 62.745 902 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 1.94 % Allowed : 15.83 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.68 (0.30), residues: 807 helix: 0.98 (0.27), residues: 387 sheet: -0.15 (0.54), residues: 104 loop : -2.46 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 99 TYR 0.012 0.002 TYR A 493 PHE 0.024 0.002 PHE A 738 TRP 0.030 0.002 TRP A 789 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6593) covalent geometry : angle 0.70826 ( 8934) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.71947 ( 2) hydrogen bonds : bond 0.03890 ( 252) hydrogen bonds : angle 4.43470 ( 725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.241 Fit side-chains REVERT: A 313 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: A 314 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7285 (tt) REVERT: A 717 GLU cc_start: 0.6565 (pm20) cc_final: 0.6177 (mt-10) REVERT: B 14 ARG cc_start: 0.7869 (mmp80) cc_final: 0.7502 (mmt180) REVERT: B 49 MET cc_start: 0.4729 (ptp) cc_final: 0.4409 (ptp) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.0767 time to fit residues: 10.7695 Evaluate side-chains 97 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.0040 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 557 GLN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.198914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175340 restraints weight = 27154.059| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 4.26 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4047 r_free = 0.4047 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6594 Z= 0.123 Angle : 0.670 14.408 8936 Z= 0.323 Chirality : 0.040 0.233 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.228 58.334 902 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.14 % Favored : 92.73 % Rotamer: Outliers : 1.94 % Allowed : 17.50 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.60 (0.30), residues: 807 helix: 1.10 (0.27), residues: 384 sheet: -0.30 (0.53), residues: 107 loop : -2.42 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 99 TYR 0.017 0.002 TYR A 493 PHE 0.030 0.001 PHE A 738 TRP 0.014 0.001 TRP A 789 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6593) covalent geometry : angle 0.66996 ( 8934) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.39271 ( 2) hydrogen bonds : bond 0.03382 ( 252) hydrogen bonds : angle 4.37024 ( 725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.252 Fit side-chains REVERT: A 313 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: A 836 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.6795 (ttt90) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.0882 time to fit residues: 12.5738 Evaluate side-chains 103 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 8 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.182384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154271 restraints weight = 31791.261| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 5.63 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6594 Z= 0.178 Angle : 0.732 14.305 8936 Z= 0.357 Chirality : 0.043 0.231 1023 Planarity : 0.005 0.052 1133 Dihedral : 6.472 60.571 902 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 2.08 % Allowed : 17.22 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.77 (0.30), residues: 807 helix: 0.90 (0.27), residues: 387 sheet: -0.46 (0.53), residues: 112 loop : -2.42 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.013 0.002 TYR A 493 PHE 0.021 0.002 PHE A 738 TRP 0.031 0.002 TRP A 789 HIS 0.003 0.001 HIS A 737 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6593) covalent geometry : angle 0.73179 ( 8934) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.63210 ( 2) hydrogen bonds : bond 0.03978 ( 252) hydrogen bonds : angle 4.50133 ( 725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.249 Fit side-chains REVERT: A 314 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 680 ASP cc_start: 0.8140 (m-30) cc_final: 0.7865 (m-30) REVERT: A 681 GLU cc_start: 0.7725 (tp30) cc_final: 0.7022 (pt0) REVERT: A 717 GLU cc_start: 0.6764 (pm20) cc_final: 0.6282 (mt-10) REVERT: A 836 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6986 (ttt90) REVERT: A 967 MET cc_start: 0.8190 (mmm) cc_final: 0.7881 (tpp) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.0961 time to fit residues: 12.2774 Evaluate side-chains 99 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 0.0470 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.195123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162421 restraints weight = 32549.458| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 8.23 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6594 Z= 0.149 Angle : 0.706 14.819 8936 Z= 0.343 Chirality : 0.042 0.235 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.412 58.623 902 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.22 % Allowed : 17.50 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.30), residues: 807 helix: 0.95 (0.27), residues: 388 sheet: -0.49 (0.53), residues: 108 loop : -2.42 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.014 0.002 TYR A 493 PHE 0.022 0.002 PHE A 738 TRP 0.019 0.002 TRP A 789 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6593) covalent geometry : angle 0.70590 ( 8934) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.61468 ( 2) hydrogen bonds : bond 0.03704 ( 252) hydrogen bonds : angle 4.45274 ( 725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.246 Fit side-chains REVERT: A 314 ILE cc_start: 0.7842 (tp) cc_final: 0.7541 (tt) REVERT: A 432 GLN cc_start: 0.5880 (mm110) cc_final: 0.5379 (tt0) REVERT: A 680 ASP cc_start: 0.7923 (m-30) cc_final: 0.7715 (m-30) REVERT: A 681 GLU cc_start: 0.7588 (tp30) cc_final: 0.6914 (pt0) REVERT: A 717 GLU cc_start: 0.6888 (pm20) cc_final: 0.6295 (mt-10) REVERT: A 967 MET cc_start: 0.8446 (mmm) cc_final: 0.8199 (tpp) REVERT: B 6 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6901 (tttt) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.0844 time to fit residues: 11.0408 Evaluate side-chains 94 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 106 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** 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 = 0.4237 r_free = 0.4237 target = 0.195661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173085 restraints weight = 23045.060| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.78 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.139 Angle : 0.686 14.982 8936 Z= 0.335 Chirality : 0.041 0.235 1023 Planarity : 0.004 0.052 1133 Dihedral : 6.276 56.920 902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.08 % Allowed : 17.36 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.70 (0.30), residues: 807 helix: 0.98 (0.27), residues: 388 sheet: -0.50 (0.53), residues: 108 loop : -2.38 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 99 TYR 0.014 0.002 TYR A 493 PHE 0.023 0.002 PHE A 738 TRP 0.018 0.001 TRP A 789 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6593) covalent geometry : angle 0.68613 ( 8934) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.50398 ( 2) hydrogen bonds : bond 0.03599 ( 252) hydrogen bonds : angle 4.43790 ( 725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.257 Fit side-chains REVERT: A 314 ILE cc_start: 0.7815 (tp) cc_final: 0.7518 (tt) REVERT: A 432 GLN cc_start: 0.5642 (mm110) cc_final: 0.5187 (tt0) REVERT: A 680 ASP cc_start: 0.7838 (m-30) cc_final: 0.7617 (m-30) REVERT: A 681 GLU cc_start: 0.7856 (tp30) cc_final: 0.7050 (pt0) REVERT: A 717 GLU cc_start: 0.6867 (pm20) cc_final: 0.6234 (mt-10) REVERT: A 967 MET cc_start: 0.7961 (mmm) cc_final: 0.7556 (tpt) outliers start: 13 outliers final: 11 residues processed: 96 average time/residue: 0.0762 time to fit residues: 10.1990 Evaluate side-chains 92 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.0970 chunk 50 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** 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 = 0.4250 r_free = 0.4250 target = 0.197099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173904 restraints weight = 24922.137| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 4.06 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6594 Z= 0.125 Angle : 0.682 15.101 8936 Z= 0.330 Chirality : 0.041 0.233 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.172 55.186 902 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 1.81 % Allowed : 17.92 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.66 (0.30), residues: 807 helix: 1.00 (0.27), residues: 388 sheet: -0.51 (0.52), residues: 108 loop : -2.34 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 99 TYR 0.014 0.001 TYR A 796 PHE 0.022 0.001 PHE A 738 TRP 0.015 0.001 TRP A 789 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6593) covalent geometry : angle 0.68242 ( 8934) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.42497 ( 2) hydrogen bonds : bond 0.03441 ( 252) hydrogen bonds : angle 4.44440 ( 725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1331.94 seconds wall clock time: 23 minutes 34.07 seconds (1414.07 seconds total)