Starting phenix.real_space_refine on Wed Feb 12 10:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_32484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_32484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_32484.map" model { file = "/net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_32484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wge_32484/02_2025/7wge_32484.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 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: 6.35, per 1000 atoms: 0.98 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: 1.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.79 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: 2.06 Time building geometry restraints manager: 1.84 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.860 ------------------------------------------------------------------------------- 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 6593 Z= 0.165 Angle : 0.631 7.401 8934 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (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 TRP 0.027 0.002 TRP A 351 HIS 0.006 0.001 HIS A 553 PHE 0.011 0.001 PHE A 454 TYR 0.007 0.001 TYR A 723 ARG 0.016 0.001 ARG A 773 *********************** 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 : 0.727 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1962 time to fit residues: 35.7459 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 31 optimal weight: 0.0010 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 714 HIS ** 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 = 0.4434 r_free = 0.4434 target = 0.216357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.192024 restraints weight = 30538.517| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 5.05 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4237 r_free = 0.4237 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4236 r_free = 0.4236 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6593 Z= 0.235 Angle : 0.704 12.548 8934 Z= 0.348 Chirality : 0.044 0.218 1023 Planarity : 0.005 0.060 1133 Dihedral : 6.278 53.053 902 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 1.67 % Allowed : 10.00 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.30), residues: 807 helix: 1.09 (0.27), residues: 367 sheet: -0.36 (0.50), residues: 112 loop : -2.20 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 703 HIS 0.004 0.001 HIS A 594 PHE 0.043 0.002 PHE A 673 TYR 0.017 0.002 TYR A 796 ARG 0.008 0.001 ARG A 773 *********************** 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 106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.776 Fit side-chains REVERT: A 717 GLU cc_start: 0.6645 (pm20) cc_final: 0.6325 (mt-10) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.2044 time to fit residues: 28.3959 Evaluate side-chains 90 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.195192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168700 restraints weight = 28348.341| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 4.97 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 6593 Z= 0.412 Angle : 0.855 11.567 8934 Z= 0.427 Chirality : 0.049 0.218 1023 Planarity : 0.006 0.050 1133 Dihedral : 7.247 74.141 902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 3.19 % Allowed : 10.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.29), residues: 807 helix: 0.41 (0.26), residues: 386 sheet: -0.67 (0.50), residues: 117 loop : -2.61 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP A 789 HIS 0.006 0.001 HIS A 720 PHE 0.021 0.003 PHE A 738 TYR 0.020 0.003 TYR A 303 ARG 0.007 0.001 ARG A 788 *********************** 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 136 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.810 Fit side-chains REVERT: A 488 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6260 (mt-10) REVERT: A 531 MET cc_start: 0.7096 (tpt) cc_final: 0.6784 (tpt) REVERT: A 579 ILE cc_start: 0.8529 (tt) cc_final: 0.8302 (tt) REVERT: A 714 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.5903 (t-90) REVERT: A 967 MET cc_start: 0.6854 (mmp) cc_final: 0.6543 (tpp) REVERT: B 14 ARG cc_start: 0.7600 (mmp80) cc_final: 0.7365 (mmt180) outliers start: 21 outliers final: 10 residues processed: 127 average time/residue: 0.2456 time to fit residues: 40.3298 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 585 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 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 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** B 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.180334 restraints weight = 24832.960| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 4.05 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4106 r_free = 0.4106 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6593 Z= 0.197 Angle : 0.678 13.802 8934 Z= 0.333 Chirality : 0.042 0.225 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.661 64.792 902 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 1.81 % Allowed : 14.72 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.30), residues: 807 helix: 0.76 (0.27), residues: 387 sheet: -0.37 (0.54), residues: 105 loop : -2.50 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 789 HIS 0.006 0.001 HIS A 310 PHE 0.024 0.002 PHE A 738 TYR 0.019 0.002 TYR A 493 ARG 0.005 0.001 ARG A 773 *********************** 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 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.672 Fit side-chains REVERT: A 314 ILE cc_start: 0.7755 (tp) cc_final: 0.7511 (tp) REVERT: A 531 MET cc_start: 0.6803 (tpt) cc_final: 0.6536 (tpt) REVERT: A 542 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 579 ILE cc_start: 0.8385 (tt) cc_final: 0.8159 (tt) REVERT: A 714 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.5929 (t-90) REVERT: B 14 ARG cc_start: 0.7360 (mmp80) cc_final: 0.7040 (mmt-90) outliers start: 11 outliers final: 8 residues processed: 104 average time/residue: 0.2083 time to fit residues: 28.1479 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 934 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.163197 restraints weight = 29894.457| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 5.78 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6593 Z= 0.320 Angle : 0.783 12.541 8934 Z= 0.385 Chirality : 0.045 0.234 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.830 65.708 902 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Rotamer: Outliers : 3.06 % Allowed : 14.86 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.30), residues: 807 helix: 0.59 (0.26), residues: 388 sheet: -0.54 (0.53), residues: 112 loop : -2.50 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.017 0.002 PHE A 673 TYR 0.014 0.002 TYR A 493 ARG 0.005 0.001 ARG B 99 *********************** 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 128 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.721 Fit side-chains REVERT: A 680 ASP cc_start: 0.7788 (m-30) cc_final: 0.7438 (m-30) outliers start: 20 outliers final: 14 residues processed: 118 average time/residue: 0.1971 time to fit residues: 31.2058 Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 HIS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU 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 39 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 557 GLN A 663 HIS ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.197108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169311 restraints weight = 30388.827| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 5.69 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3955 r_free = 0.3955 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6593 Z= 0.190 Angle : 0.696 15.469 8934 Z= 0.340 Chirality : 0.041 0.226 1023 Planarity : 0.004 0.049 1133 Dihedral : 6.430 57.749 902 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.39 % Favored : 92.36 % Rotamer: Outliers : 2.22 % Allowed : 17.36 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 807 helix: 0.78 (0.27), residues: 388 sheet: -0.44 (0.53), residues: 107 loop : -2.47 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 789 HIS 0.002 0.001 HIS A 663 PHE 0.017 0.001 PHE A 738 TYR 0.017 0.002 TYR A 796 ARG 0.007 0.001 ARG B 99 *********************** 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 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.831 Fit side-chains REVERT: A 314 ILE cc_start: 0.7844 (tp) cc_final: 0.7511 (tt) REVERT: A 579 ILE cc_start: 0.8545 (tt) cc_final: 0.8261 (tt) REVERT: A 680 ASP cc_start: 0.7843 (m-30) cc_final: 0.7561 (m-30) REVERT: A 691 HIS cc_start: 0.6519 (m90) cc_final: 0.6298 (m90) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.1905 time to fit residues: 25.8145 Evaluate side-chains 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU 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 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 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 = 0.4208 r_free = 0.4208 target = 0.191773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160117 restraints weight = 27690.070| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 7.32 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 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 = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6593 Z= 0.301 Angle : 0.738 14.231 8934 Z= 0.364 Chirality : 0.044 0.221 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.660 61.888 902 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 2.50 % Allowed : 17.50 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.30), residues: 807 helix: 0.61 (0.27), residues: 387 sheet: -0.60 (0.53), residues: 112 loop : -2.47 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.015 0.002 PHE A 673 TYR 0.013 0.002 TYR A 493 ARG 0.006 0.001 ARG A 328 *********************** 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 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.722 Fit side-chains REVERT: A 314 ILE cc_start: 0.8042 (tp) cc_final: 0.7759 (tt) REVERT: A 432 GLN cc_start: 0.5941 (mm110) cc_final: 0.5406 (tt0) REVERT: A 534 MET cc_start: 0.7985 (mtp) cc_final: 0.7631 (mtp) REVERT: A 592 ARG cc_start: 0.7219 (mpt-90) cc_final: 0.6538 (ttp80) REVERT: A 680 ASP cc_start: 0.7806 (m-30) cc_final: 0.7502 (m-30) outliers start: 16 outliers final: 15 residues processed: 103 average time/residue: 0.2154 time to fit residues: 29.3675 Evaluate side-chains 106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 706 SER Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.195040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163559 restraints weight = 27400.179| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 7.59 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3875 r_free = 0.3875 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6593 Z= 0.194 Angle : 0.711 14.811 8934 Z= 0.347 Chirality : 0.041 0.222 1023 Planarity : 0.004 0.049 1133 Dihedral : 6.430 56.956 902 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.77 % Favored : 92.11 % Rotamer: Outliers : 2.22 % Allowed : 18.33 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 807 helix: 0.76 (0.27), residues: 387 sheet: -0.48 (0.53), residues: 107 loop : -2.44 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 789 HIS 0.002 0.001 HIS A 737 PHE 0.014 0.001 PHE A 629 TYR 0.016 0.001 TYR A 796 ARG 0.007 0.000 ARG B 99 *********************** 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 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.737 Fit side-chains REVERT: A 314 ILE cc_start: 0.7971 (tp) cc_final: 0.7690 (tt) REVERT: A 432 GLN cc_start: 0.5850 (mm110) cc_final: 0.5320 (tt0) REVERT: A 534 MET cc_start: 0.7913 (mtp) cc_final: 0.7692 (mtp) REVERT: A 579 ILE cc_start: 0.8338 (tt) cc_final: 0.8061 (tt) REVERT: A 592 ARG cc_start: 0.7083 (mpt-90) cc_final: 0.6380 (ttp80) REVERT: A 633 MET cc_start: 0.7960 (ttm) cc_final: 0.7676 (mtp) REVERT: A 680 ASP cc_start: 0.7436 (m-30) cc_final: 0.7105 (m-30) REVERT: A 936 ASP cc_start: 0.6899 (m-30) cc_final: 0.6621 (m-30) outliers start: 14 outliers final: 14 residues processed: 106 average time/residue: 0.1942 time to fit residues: 27.4198 Evaluate side-chains 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 706 SER Chi-restraints excluded: chain A residue 714 HIS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 887 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.195279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.172075 restraints weight = 24501.520| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.95 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6593 Z= 0.189 Angle : 0.680 14.833 8934 Z= 0.334 Chirality : 0.041 0.214 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.251 55.859 902 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.08 % Allowed : 18.19 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 807 helix: 0.84 (0.27), residues: 388 sheet: -0.42 (0.53), residues: 107 loop : -2.40 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 789 HIS 0.002 0.001 HIS A 720 PHE 0.011 0.001 PHE A 629 TYR 0.015 0.001 TYR A 796 ARG 0.007 0.001 ARG A 298 *********************** 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 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.781 Fit side-chains REVERT: A 314 ILE cc_start: 0.7935 (tp) cc_final: 0.7602 (tt) REVERT: A 432 GLN cc_start: 0.5705 (mm110) cc_final: 0.5195 (tt0) REVERT: A 534 MET cc_start: 0.8167 (mtp) cc_final: 0.7846 (mtp) REVERT: A 579 ILE cc_start: 0.8493 (tt) cc_final: 0.8219 (tt) REVERT: A 592 ARG cc_start: 0.6939 (mpt-90) cc_final: 0.6316 (ttp80) REVERT: A 680 ASP cc_start: 0.7647 (m-30) cc_final: 0.7410 (m-30) REVERT: A 717 GLU cc_start: 0.6855 (pm20) cc_final: 0.6218 (mt-10) outliers start: 13 outliers final: 13 residues processed: 101 average time/residue: 0.1957 time to fit residues: 26.5091 Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 706 SER Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 32 optimal weight: 0.0040 chunk 67 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.7452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4240 r_free = 0.4240 target = 0.195676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.172481 restraints weight = 27528.792| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.13 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4022 r_free = 0.4022 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6593 Z= 0.195 Angle : 0.691 15.197 8934 Z= 0.339 Chirality : 0.041 0.224 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.228 55.842 902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 2.50 % Allowed : 17.92 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.30), residues: 807 helix: 0.90 (0.27), residues: 388 sheet: -0.40 (0.53), residues: 107 loop : -2.37 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 789 HIS 0.002 0.001 HIS A 594 PHE 0.009 0.001 PHE A 756 TYR 0.015 0.001 TYR A 796 ARG 0.010 0.001 ARG B 99 ********************** 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 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.697 Fit side-chains REVERT: A 314 ILE cc_start: 0.7907 (tp) cc_final: 0.7566 (tt) REVERT: A 432 GLN cc_start: 0.5736 (mm110) cc_final: 0.5208 (tt0) REVERT: A 534 MET cc_start: 0.8142 (mtp) cc_final: 0.7822 (mtp) REVERT: A 579 ILE cc_start: 0.8488 (tt) cc_final: 0.8235 (tt) REVERT: A 592 ARG cc_start: 0.6953 (mpt-90) cc_final: 0.6343 (ttp80) REVERT: A 622 ILE cc_start: 0.8465 (pt) cc_final: 0.8190 (mt) REVERT: A 680 ASP cc_start: 0.7637 (m-30) cc_final: 0.7387 (m-30) REVERT: A 717 GLU cc_start: 0.6884 (pm20) cc_final: 0.6291 (mt-10) REVERT: A 967 MET cc_start: 0.8064 (mmm) cc_final: 0.7630 (tpp) outliers start: 16 outliers final: 13 residues processed: 101 average time/residue: 0.1806 time to fit residues: 24.7496 Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 706 SER Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4256 r_free = 0.4256 target = 0.197151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173293 restraints weight = 26194.978| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 4.22 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3964 r_free = 0.3964 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3964 r_free = 0.3964 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6593 Z= 0.180 Angle : 0.685 15.160 8934 Z= 0.334 Chirality : 0.041 0.217 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.143 54.897 902 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 2.22 % Allowed : 18.19 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.30), residues: 807 helix: 0.98 (0.27), residues: 388 sheet: -0.31 (0.53), residues: 105 loop : -2.34 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 789 HIS 0.002 0.001 HIS A 720 PHE 0.013 0.001 PHE A 629 TYR 0.014 0.001 TYR A 796 ARG 0.010 0.001 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.54 seconds wall clock time: 46 minutes 44.56 seconds (2804.56 seconds total)