Starting phenix.real_space_refine on Fri Jun 6 12:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wge_32484/06_2025/7wge_32484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wge_32484/06_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_32484/06_2025/7wge_32484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wge_32484/06_2025/7wge_32484.map" model { file = "/net/cci-nas-00/data/ceres_data/7wge_32484/06_2025/7wge_32484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wge_32484/06_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-5710/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: 7.09, per 1000 atoms: 1.10 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: 1.86 Conformation dependent library (CDL) restraints added in 1.6 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: 0.86 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: 1.89 Time building geometry restraints manager: 2.10 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: 0.010 Normalize map: mean=0, sd=1: 5.480 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:3.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6594 Z= 0.120 Angle : 0.631 7.401 8936 Z= 0.315 Chirality : 0.040 0.213 1023 Planarity : 0.005 0.078 1133 Dihedral : 15.024 89.613 2509 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.16232 ( 252) hydrogen bonds : angle 5.77633 ( 725) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.59911 ( 2) covalent geometry : bond 0.00258 ( 6593) covalent geometry : angle 0.63074 ( 8934) *********************** 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 : 0.757 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1933 time to fit residues: 35.3030 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 : 0.679 ------------------------------------------------------------------------------- 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 6594 Z= 0.162 Angle : 0.704 12.548 8936 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 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 252) hydrogen bonds : angle 4.86602 ( 725) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.41176 ( 2) covalent geometry : bond 0.00371 ( 6593) covalent geometry : angle 0.70376 ( 8934) *********************** 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 : 0.709 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: 0.2127 time to fit residues: 29.5914 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 : 0.755 ------------------------------------------------------------------------------- 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 6594 Z= 0.171 Angle : 0.697 12.224 8936 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 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 252) hydrogen bonds : angle 4.64162 ( 725) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.40525 ( 2) covalent geometry : bond 0.00409 ( 6593) covalent geometry : angle 0.69734 ( 8934) *********************** 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 : 1.129 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: 0.2955 time to fit residues: 44.4863 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 : 0.797 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.204909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181538 restraints weight = 24962.648| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 4.19 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4111 r_free = 0.4111 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6594 Z= 0.125 Angle : 0.646 13.658 8936 Z= 0.316 Chirality : 0.041 0.226 1023 Planarity : 0.005 0.051 1133 Dihedral : 6.367 62.847 902 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.52 % Favored : 92.23 % 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: -0.67 (0.30), residues: 807 helix: 1.04 (0.27), residues: 381 sheet: -0.36 (0.52), residues: 110 loop : -2.41 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 789 HIS 0.003 0.001 HIS A 663 PHE 0.030 0.002 PHE A 738 TYR 0.015 0.001 TYR A 796 ARG 0.005 0.000 ARG A 836 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 252) hydrogen bonds : angle 4.43356 ( 725) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.39367 ( 2) covalent geometry : bond 0.00290 ( 6593) covalent geometry : angle 0.64642 ( 8934) *********************** 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 : 0.957 Fit side-chains REVERT: A 313 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7161 (tt0) REVERT: A 314 ILE cc_start: 0.7492 (tp) cc_final: 0.7243 (tp) REVERT: A 579 ILE cc_start: 0.8581 (tt) cc_final: 0.8333 (tt) REVERT: A 714 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.5902 (t-90) REVERT: A 717 GLU cc_start: 0.6466 (pm20) cc_final: 0.6120 (mt-10) REVERT: A 771 GLU cc_start: 0.7727 (tp30) cc_final: 0.7184 (tp30) REVERT: A 799 ILE cc_start: 0.8493 (tp) cc_final: 0.8052 (tp) REVERT: B 49 MET cc_start: 0.4763 (ptp) cc_final: 0.4529 (ptp) outliers start: 18 outliers final: 9 residues processed: 113 average time/residue: 0.2161 time to fit residues: 32.6557 Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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: 0.0000 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.196983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165297 restraints weight = 29406.581| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 7.52 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6594 Z= 0.177 Angle : 0.744 14.012 8936 Z= 0.361 Chirality : 0.044 0.221 1023 Planarity : 0.005 0.052 1133 Dihedral : 6.612 64.714 902 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 3.33 % Allowed : 13.75 % Favored : 82.92 % 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: 0.85 (0.27), residues: 388 sheet: -0.27 (0.54), residues: 105 loop : -2.46 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 789 HIS 0.004 0.001 HIS A 594 PHE 0.024 0.002 PHE A 738 TYR 0.025 0.002 TYR A 303 ARG 0.006 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 252) hydrogen bonds : angle 4.56905 ( 725) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.61080 ( 2) covalent geometry : bond 0.00430 ( 6593) covalent geometry : angle 0.74356 ( 8934) *********************** 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 125 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.734 Fit side-chains REVERT: A 313 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 531 MET cc_start: 0.6887 (tpt) cc_final: 0.6632 (tpt) REVERT: A 579 ILE cc_start: 0.8310 (tt) cc_final: 0.8063 (tt) REVERT: A 714 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.5866 (t-90) REVERT: A 914 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.5920 (mt) REVERT: A 967 MET cc_start: 0.8417 (mmm) cc_final: 0.7932 (tpp) REVERT: B 49 MET cc_start: 0.4797 (ptp) cc_final: 0.4548 (ptp) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.1683 time to fit residues: 26.4441 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 : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 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 914 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.182271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154405 restraints weight = 30104.506| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 5.61 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6594 Z= 0.185 Angle : 0.724 13.758 8936 Z= 0.357 Chirality : 0.044 0.223 1023 Planarity : 0.005 0.050 1133 Dihedral : 6.720 62.095 902 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 2.92 % Allowed : 15.42 % Favored : 81.67 % 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: 0.74 (0.27), residues: 388 sheet: -0.34 (0.54), residues: 107 loop : -2.42 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 789 HIS 0.003 0.001 HIS A 623 PHE 0.029 0.002 PHE A 738 TYR 0.014 0.002 TYR A 796 ARG 0.008 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 252) hydrogen bonds : angle 4.59415 ( 725) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.68669 ( 2) covalent geometry : bond 0.00452 ( 6593) covalent geometry : angle 0.72441 ( 8934) *********************** 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 122 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.720 Fit side-chains REVERT: A 314 ILE cc_start: 0.7920 (tp) cc_final: 0.7278 (tt) REVERT: A 579 ILE cc_start: 0.8600 (tt) cc_final: 0.8343 (tt) REVERT: A 717 GLU cc_start: 0.6701 (pm20) cc_final: 0.6270 (mt-10) REVERT: B 49 MET cc_start: 0.4793 (ptp) cc_final: 0.4491 (ptp) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.1800 time to fit residues: 27.6449 Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4237 r_free = 0.4237 target = 0.195332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.168530 restraints weight = 27653.868| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 5.30 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.165 | | 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: 0.7110 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6594 Z= 0.151 Angle : 0.706 14.667 8936 Z= 0.343 Chirality : 0.042 0.227 1023 Planarity : 0.005 0.051 1133 Dihedral : 6.511 59.999 902 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.77 % Favored : 92.11 % Rotamer: Outliers : 2.36 % Allowed : 17.36 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.27), residues: 389 sheet: -0.47 (0.53), residues: 107 loop : -2.41 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 789 HIS 0.003 0.001 HIS B 4 PHE 0.021 0.002 PHE A 738 TYR 0.015 0.001 TYR A 796 ARG 0.008 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 252) hydrogen bonds : angle 4.52323 ( 725) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.49108 ( 2) covalent geometry : bond 0.00362 ( 6593) covalent geometry : angle 0.70579 ( 8934) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.756 Fit side-chains REVERT: A 314 ILE cc_start: 0.7956 (tp) cc_final: 0.7409 (tt) REVERT: A 432 GLN cc_start: 0.5854 (mm110) cc_final: 0.5366 (tt0) REVERT: A 579 ILE cc_start: 0.8554 (tt) cc_final: 0.8280 (tt) REVERT: A 680 ASP cc_start: 0.8040 (m-30) cc_final: 0.7750 (m-30) outliers start: 15 outliers final: 14 residues processed: 103 average time/residue: 0.1803 time to fit residues: 25.3185 Evaluate side-chains 109 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 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 914 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.196750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171038 restraints weight = 27459.912| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 4.95 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6594 Z= 0.129 Angle : 0.675 14.564 8936 Z= 0.332 Chirality : 0.041 0.216 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.248 56.150 902 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.77 % Favored : 92.11 % Rotamer: Outliers : 2.64 % Allowed : 16.81 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 386 sheet: -0.40 (0.53), residues: 107 loop : -2.40 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 789 HIS 0.002 0.001 HIS A 775 PHE 0.024 0.001 PHE A 738 TYR 0.017 0.001 TYR A 796 ARG 0.007 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 252) hydrogen bonds : angle 4.41679 ( 725) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.34374 ( 2) covalent geometry : bond 0.00299 ( 6593) covalent geometry : angle 0.67460 ( 8934) *********************** 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 113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.646 Fit side-chains REVERT: A 314 ILE cc_start: 0.7999 (tp) cc_final: 0.7543 (tt) REVERT: A 432 GLN cc_start: 0.5782 (mm110) cc_final: 0.5314 (tt0) REVERT: A 579 ILE cc_start: 0.8520 (tt) cc_final: 0.8267 (tt) REVERT: A 680 ASP cc_start: 0.7845 (m-30) cc_final: 0.7576 (m-30) REVERT: A 717 GLU cc_start: 0.6843 (pm20) cc_final: 0.6258 (mt-10) outliers start: 17 outliers final: 16 residues processed: 106 average time/residue: 0.1792 time to fit residues: 25.9983 Evaluate side-chains 105 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 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 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: 0.6980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.195069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.172025 restraints weight = 24528.823| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.88 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3956 r_free = 0.3956 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 = 0.3956 r_free = 0.3956 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6594 Z= 0.155 Angle : 0.712 14.627 8936 Z= 0.348 Chirality : 0.042 0.231 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.335 58.033 902 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.50 % Allowed : 17.78 % 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: -0.77 (0.30), residues: 807 helix: 0.88 (0.27), residues: 388 sheet: -0.42 (0.53), residues: 107 loop : -2.40 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 789 HIS 0.007 0.001 HIS B 4 PHE 0.018 0.002 PHE A 738 TYR 0.014 0.001 TYR A 796 ARG 0.007 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 252) hydrogen bonds : angle 4.48979 ( 725) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.51375 ( 2) covalent geometry : bond 0.00371 ( 6593) covalent geometry : angle 0.71234 ( 8934) *********************** 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 : 0.774 Fit side-chains REVERT: A 314 ILE cc_start: 0.8100 (tp) cc_final: 0.7705 (tt) REVERT: A 432 GLN cc_start: 0.5630 (mm110) cc_final: 0.5171 (tt0) REVERT: A 579 ILE cc_start: 0.8508 (tt) cc_final: 0.8223 (tt) REVERT: A 633 MET cc_start: 0.8026 (ttm) cc_final: 0.7722 (mtp) REVERT: A 680 ASP cc_start: 0.7786 (m-30) cc_final: 0.7521 (m-30) REVERT: A 717 GLU cc_start: 0.6828 (pm20) cc_final: 0.6245 (mt-10) REVERT: A 967 MET cc_start: 0.7973 (mmm) cc_final: 0.7669 (tpp) outliers start: 16 outliers final: 16 residues processed: 103 average time/residue: 0.1870 time to fit residues: 26.9617 Evaluate side-chains 108 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 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 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: 0.8980 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 32 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.195217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170140 restraints weight = 27594.217| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.55 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6594 Z= 0.149 Angle : 0.703 15.042 8936 Z= 0.345 Chirality : 0.042 0.231 1023 Planarity : 0.004 0.050 1133 Dihedral : 6.373 57.598 902 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 2.64 % Allowed : 17.50 % Favored : 79.86 % 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: 0.87 (0.27), residues: 388 sheet: -0.37 (0.54), residues: 105 loop : -2.33 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 789 HIS 0.002 0.001 HIS A 594 PHE 0.019 0.002 PHE A 738 TYR 0.014 0.001 TYR A 796 ARG 0.006 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 252) hydrogen bonds : angle 4.50344 ( 725) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.56305 ( 2) covalent geometry : bond 0.00357 ( 6593) covalent geometry : angle 0.70253 ( 8934) ********************** 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 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.720 Fit side-chains REVERT: A 314 ILE cc_start: 0.8139 (tp) cc_final: 0.7763 (tt) REVERT: A 432 GLN cc_start: 0.5744 (mm110) cc_final: 0.5163 (tt0) REVERT: A 579 ILE cc_start: 0.8549 (tt) cc_final: 0.8280 (tt) REVERT: A 680 ASP cc_start: 0.7669 (m-30) cc_final: 0.7402 (m-30) REVERT: A 967 MET cc_start: 0.8109 (mmm) cc_final: 0.7744 (tpp) REVERT: B 75 MET cc_start: 0.8136 (mpp) cc_final: 0.7885 (ptp) REVERT: B 91 SER cc_start: 0.8336 (m) cc_final: 0.7917 (t) outliers start: 17 outliers final: 17 residues processed: 103 average time/residue: 0.1838 time to fit residues: 26.2724 Evaluate side-chains 106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 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 758 ILE 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: 3.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** A 887 GLN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.193236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168624 restraints weight = 26310.866| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.38 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6594 Z= 0.163 Angle : 0.716 15.087 8936 Z= 0.351 Chirality : 0.043 0.227 1023 Planarity : 0.004 0.051 1133 Dihedral : 6.471 58.887 902 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.40 % Favored : 91.48 % Rotamer: Outliers : 2.78 % Allowed : 17.92 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.30), residues: 807 helix: 0.88 (0.27), residues: 388 sheet: -0.42 (0.54), residues: 105 loop : -2.37 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 789 HIS 0.003 0.001 HIS A 594 PHE 0.016 0.002 PHE A 738 TYR 0.012 0.002 TYR A 796 ARG 0.006 0.001 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 252) hydrogen bonds : angle 4.53976 ( 725) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.63270 ( 2) covalent geometry : bond 0.00393 ( 6593) covalent geometry : angle 0.71589 ( 8934) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.39 seconds wall clock time: 54 minutes 2.16 seconds (3242.16 seconds total)