Starting phenix.real_space_refine on Wed Mar 12 10:09:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wge_32484/03_2025/7wge_32484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wge_32484/03_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_32484/03_2025/7wge_32484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2025/7wge_32484.map" model { file = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_2025/7wge_32484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wge_32484/03_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-5624/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: 7.04, per 1000 atoms: 1.09 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: 1.60 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: 0.73 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: 1.81 Time building geometry restraints manager: 1.91 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: 0.340 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.180 Find NCS groups from input model: 0.060 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- 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 : 0.778 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1905 time to fit residues: 34.8281 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 : 0.703 ------------------------------------------------------------------------------- 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 = 0.192036 restraints weight = 30538.493| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 5.05 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- 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 : 0.703 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: 0.1890 time to fit residues: 26.0608 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 : 0.673 ------------------------------------------------------------------------------- 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: 6.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 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 = 0.4338 r_free = 0.4338 target = 0.205623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.179796 restraints weight = 28287.352| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 5.07 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6593 Z= 0.260 Angle : 0.697 12.224 8934 Z= 0.346 Chirality : 0.043 0.212 1023 Planarity : 0.005 0.052 1133 Dihedral : 6.663 67.225 902 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.52 % Favored : 92.23 % Rotamer: Outliers : 2.22 % Allowed : 11.53 % 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: -0.77 (0.30), residues: 807 helix: 0.92 (0.27), residues: 377 sheet: -0.37 (0.51), residues: 110 loop : -2.39 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 789 HIS 0.003 0.001 HIS A 594 PHE 0.028 0.002 PHE A 738 TYR 0.023 0.002 TYR A 303 ARG 0.007 0.001 ARG A 773 *********************** 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 122 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 1.118 Fit side-chains REVERT: A 313 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: A 359 ASP cc_start: 0.6189 (p0) cc_final: 0.5970 (p0) REVERT: A 579 ILE cc_start: 0.8658 (tt) cc_final: 0.8441 (tt) REVERT: A 771 GLU cc_start: 0.7749 (tp30) cc_final: 0.7116 (tp30) REVERT: A 799 ILE cc_start: 0.8348 (tp) cc_final: 0.7972 (tp) outliers start: 14 outliers final: 9 residues processed: 114 average time/residue: 0.3430 time to fit residues: 51.6876 Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 574 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP 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 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.205545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.182926 restraints weight = 25024.671| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 4.06 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4130 r_free = 0.4130 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6593 Z= 0.173 Angle : 0.641 13.792 8934 Z= 0.313 Chirality : 0.041 0.227 1023 Planarity : 0.005 0.051 1133 Dihedral : 6.316 62.006 902 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.27 % Favored : 92.48 % Rotamer: Outliers : 2.78 % Allowed : 12.78 % Favored : 84.44 % 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: -0.65 (0.30), residues: 807 helix: 1.07 (0.27), residues: 381 sheet: -0.34 (0.52), residues: 110 loop : -2.41 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 789 HIS 0.004 0.001 HIS A 663 PHE 0.032 0.002 PHE A 738 TYR 0.015 0.001 TYR A 796 ARG 0.005 0.000 ARG A 836 *********************** 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 121 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.835 Fit side-chains REVERT: A 313 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: A 314 ILE cc_start: 0.7484 (tp) cc_final: 0.7234 (tp) REVERT: A 579 ILE cc_start: 0.8567 (tt) cc_final: 0.8319 (tt) REVERT: A 714 HIS cc_start: 0.6436 (OUTLIER) cc_final: 0.5924 (t-90) REVERT: A 717 GLU cc_start: 0.6449 (pm20) cc_final: 0.6126 (mt-10) REVERT: A 771 GLU cc_start: 0.7740 (tp30) cc_final: 0.7200 (tp30) REVERT: A 799 ILE cc_start: 0.8488 (tp) cc_final: 0.8053 (tp) REVERT: B 49 MET cc_start: 0.4718 (ptp) cc_final: 0.4484 (ptp) outliers start: 18 outliers final: 10 residues processed: 113 average time/residue: 0.2398 time to fit residues: 36.6334 Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.0030 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.195454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161614 restraints weight = 29490.526| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 8.70 r_work: 0.3280 rms_B_bonded: 8.50 restraints_weight: 2.0000 r_work: 0.3458 rms_B_bonded: 5.22 restraints_weight: 4.0000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6593 Z= 0.346 Angle : 0.770 14.618 8934 Z= 0.374 Chirality : 0.045 0.219 1023 Planarity : 0.005 0.051 1133 Dihedral : 6.766 66.609 902 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 3.19 % Allowed : 13.75 % Favored : 83.06 % 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: -0.87 (0.30), residues: 807 helix: 0.76 (0.27), residues: 387 sheet: -0.43 (0.52), residues: 112 loop : -2.43 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.023 0.002 PHE A 738 TYR 0.023 0.002 TYR A 303 ARG 0.007 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 127 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.064 Fit side-chains REVERT: A 314 ILE cc_start: 0.8036 (tp) cc_final: 0.7807 (tp) REVERT: A 488 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 531 MET cc_start: 0.7831 (tpt) cc_final: 0.7446 (tpt) REVERT: A 542 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 579 ILE cc_start: 0.8495 (tt) cc_final: 0.8272 (tt) REVERT: A 714 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.5969 (t-90) REVERT: A 914 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.5886 (mt) REVERT: B 100 ASN cc_start: 0.6560 (m110) cc_final: 0.6326 (p0) outliers start: 21 outliers final: 14 residues processed: 116 average time/residue: 0.2759 time to fit residues: 43.4629 Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.917 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 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 914 LEU 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 106 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.194733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165842 restraints weight = 30588.365| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 6.27 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 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 = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6593 Z= 0.276 Angle : 0.726 14.987 8934 Z= 0.353 Chirality : 0.043 0.232 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.708 62.410 902 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.27 % Favored : 91.48 % Rotamer: Outliers : 3.06 % Allowed : 15.97 % Favored : 80.97 % 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: 0.74 (0.27), residues: 386 sheet: -0.48 (0.53), residues: 112 loop : -2.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 789 HIS 0.003 0.001 HIS A 623 PHE 0.027 0.002 PHE A 738 TYR 0.029 0.002 TYR A 303 ARG 0.009 0.001 ARG A 298 *********************** 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 125 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.704 Fit side-chains REVERT: A 579 ILE cc_start: 0.8430 (tt) cc_final: 0.8155 (tt) REVERT: A 717 GLU cc_start: 0.6761 (pm20) cc_final: 0.6192 (mt-10) outliers start: 20 outliers final: 16 residues processed: 113 average time/residue: 0.1788 time to fit residues: 27.2136 Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 937 VAL 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 106 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.193679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168605 restraints weight = 27773.220| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.56 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6593 Z= 0.248 Angle : 0.713 14.585 8934 Z= 0.347 Chirality : 0.042 0.215 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.572 60.688 902 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.15 % Favored : 91.60 % Rotamer: Outliers : 2.36 % Allowed : 17.50 % Favored : 80.14 % 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: -0.88 (0.30), residues: 807 helix: 0.81 (0.27), residues: 388 sheet: -0.48 (0.54), residues: 107 loop : -2.48 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 789 HIS 0.002 0.001 HIS A 737 PHE 0.017 0.002 PHE A 738 TYR 0.022 0.002 TYR A 303 ARG 0.007 0.001 ARG B 99 *********************** 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: 15 poor density : 95 time to evaluate : 0.653 Fit side-chains REVERT: A 314 ILE cc_start: 0.7824 (tp) cc_final: 0.7510 (tt) REVERT: A 432 GLN cc_start: 0.5839 (mm110) cc_final: 0.5365 (tt0) REVERT: A 579 ILE cc_start: 0.8556 (tt) cc_final: 0.8294 (tt) outliers start: 15 outliers final: 14 residues processed: 103 average time/residue: 0.1898 time to fit residues: 26.0361 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER 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 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 914 LEU Chi-restraints excluded: chain A residue 954 ILE 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 72 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 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 = 0.4242 r_free = 0.4242 target = 0.196239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.172528 restraints weight = 27405.182| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 4.26 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 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 = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6593 Z= 0.184 Angle : 0.679 15.536 8934 Z= 0.329 Chirality : 0.041 0.234 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.285 56.466 902 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % 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: -0.74 (0.30), residues: 807 helix: 0.94 (0.27), residues: 389 sheet: -0.47 (0.53), residues: 107 loop : -2.42 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 789 HIS 0.008 0.001 HIS B 4 PHE 0.022 0.001 PHE A 738 TYR 0.019 0.002 TYR A 303 ARG 0.006 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 : 0.701 Fit side-chains REVERT: A 314 ILE cc_start: 0.7775 (tp) cc_final: 0.7493 (tt) REVERT: A 432 GLN cc_start: 0.5760 (mm110) cc_final: 0.5285 (tt0) REVERT: A 579 ILE cc_start: 0.8507 (tt) cc_final: 0.8241 (tt) REVERT: A 680 ASP cc_start: 0.7906 (m-30) cc_final: 0.7629 (m-30) REVERT: A 717 GLU cc_start: 0.6768 (pm20) cc_final: 0.6187 (mt-10) outliers start: 14 outliers final: 14 residues processed: 105 average time/residue: 0.1615 time to fit residues: 23.4410 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 : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 914 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 954 ILE 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 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 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 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172858 restraints weight = 24495.315| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.93 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4000 r_free = 0.4000 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5286 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= 0.209 Angle : 0.683 15.362 8934 Z= 0.329 Chirality : 0.042 0.233 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.260 57.254 902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % Rotamer: Outliers : 2.50 % Allowed : 18.75 % Favored : 78.75 % 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: -0.73 (0.30), residues: 807 helix: 0.94 (0.27), residues: 389 sheet: -0.42 (0.53), residues: 107 loop : -2.42 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 789 HIS 0.003 0.001 HIS A 737 PHE 0.017 0.001 PHE A 738 TYR 0.018 0.002 TYR A 303 ARG 0.007 0.001 ARG B 99 *********************** 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 109 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.735 Fit side-chains REVERT: A 314 ILE cc_start: 0.7804 (tp) cc_final: 0.7528 (tt) REVERT: A 432 GLN cc_start: 0.5684 (mm110) cc_final: 0.5215 (tt0) REVERT: A 579 ILE cc_start: 0.8498 (tt) cc_final: 0.8234 (tt) REVERT: A 680 ASP cc_start: 0.7856 (m-30) cc_final: 0.7592 (m-30) REVERT: A 717 GLU cc_start: 0.6824 (pm20) cc_final: 0.6232 (mt-10) REVERT: A 967 MET cc_start: 0.7932 (mmm) cc_final: 0.7509 (tpt) outliers start: 16 outliers final: 15 residues processed: 102 average time/residue: 0.1646 time to fit residues: 23.2832 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP 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 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 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 57 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 0.0870 chunk 67 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- 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 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 = 0.4269 r_free = 0.4269 target = 0.198903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.175074 restraints weight = 27557.303| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 4.32 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6593 Z= 0.172 Angle : 0.681 15.625 8934 Z= 0.329 Chirality : 0.041 0.235 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.073 55.020 902 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % Rotamer: Outliers : 1.94 % Allowed : 19.31 % Favored : 78.75 % 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: -0.56 (0.30), residues: 807 helix: 1.10 (0.27), residues: 388 sheet: -0.40 (0.52), residues: 107 loop : -2.34 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 789 HIS 0.002 0.001 HIS A 310 PHE 0.020 0.001 PHE A 738 TYR 0.017 0.001 TYR A 303 ARG 0.009 0.000 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 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.774 Fit side-chains REVERT: A 314 ILE cc_start: 0.7760 (tp) cc_final: 0.7487 (tt) REVERT: A 362 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7709 (mm-40) REVERT: A 432 GLN cc_start: 0.5652 (mm110) cc_final: 0.5165 (tt0) REVERT: A 531 MET cc_start: 0.7113 (tpt) cc_final: 0.6775 (tpt) REVERT: A 579 ILE cc_start: 0.8479 (tt) cc_final: 0.8224 (tt) REVERT: A 622 ILE cc_start: 0.8225 (pt) cc_final: 0.7894 (mt) REVERT: A 680 ASP cc_start: 0.7821 (m-30) cc_final: 0.7528 (m-30) REVERT: A 696 GLN cc_start: 0.6938 (tp40) cc_final: 0.6607 (mp10) REVERT: A 717 GLU cc_start: 0.6825 (pm20) cc_final: 0.6415 (mt-10) REVERT: A 967 MET cc_start: 0.8011 (mmm) cc_final: 0.7616 (tpp) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.1582 time to fit residues: 23.0324 Evaluate side-chains 106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 789 TRP 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: 2.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.0040 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 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 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 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 = 0.4250 r_free = 0.4250 target = 0.197325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.172329 restraints weight = 26420.965| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 4.63 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 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 = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6593 Z= 0.185 Angle : 0.676 15.373 8934 Z= 0.330 Chirality : 0.042 0.232 1023 Planarity : 0.004 0.049 1133 Dihedral : 6.080 54.557 902 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.52 % Favored : 92.36 % Rotamer: Outliers : 1.94 % Allowed : 18.89 % Favored : 79.17 % 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: -0.56 (0.30), residues: 807 helix: 1.04 (0.27), residues: 388 sheet: -0.35 (0.53), residues: 107 loop : -2.26 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 789 HIS 0.002 0.001 HIS A 594 PHE 0.016 0.001 PHE A 738 TYR 0.017 0.001 TYR A 303 ARG 0.010 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.04 seconds wall clock time: 56 minutes 5.07 seconds (3365.07 seconds total)