Starting phenix.real_space_refine on Thu Jul 2 07:58:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wge_32484/07_2026/7wge_32484.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1495 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4099 2.51 5 N 1121 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6460 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5600 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 698, 5563 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 5630 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 828 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.20, per 1000 atoms: 0.34 Number of scatterers: 6460 At special positions: 0 Unit cell: (68.475, 92.13, 140.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 3 15.00 Mg 1 11.99 O 1189 8.00 N 1121 7.00 C 4099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 35 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 406.8 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1542 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 49.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 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: 0.93 Time building geometry restraints manager: 0.49 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: 3624 17.92 - 35.85: 327 35.85 - 53.77: 63 53.77 - 71.69: 21 71.69 - 89.61: 8 Dihedral angle restraints: 4043 sinusoidal: 1669 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 4040 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 : 14.846 89.613 2498 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.30), residues: 807 helix: 1.54 (0.28), residues: 344 sheet: -0.37 (0.52), residues: 111 loop : -2.23 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 773 TYR 0.007 0.001 TYR A 723 PHE 0.011 0.001 PHE A 454 TRP 0.027 0.002 TRP A 351 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 6593) covalent geometry : angle 0.63074 / 0.32 ( 8934) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 0.59911 / 0.35 ( 2) hydrogen bonds : bond 0.16232 / 11.50 ( 252) hydrogen bonds : angle 5.77633 / 3.97 ( 725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0677 time to fit residues: 12.5170 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 : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.216467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.194906 restraints weight = 26431.610| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 4.09 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4247 r_free = 0.4247 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2240 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= 0.162 Angle : 0.724 13.939 8936 Z= 0.356 Chirality : 0.044 0.218 1023 Planarity : 0.005 0.059 1133 Dihedral : 5.336 54.632 891 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.77 % Favored : 91.98 % Rotamer: Outliers : 1.81 % Allowed : 10.00 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.30), residues: 807 helix: 1.02 (0.27), residues: 365 sheet: -0.41 (0.50), residues: 112 loop : -2.14 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 773 TYR 0.012 0.002 TYR A 796 PHE 0.055 0.002 PHE A 673 TRP 0.019 0.002 TRP A 703 HIS 0.004 0.001 HIS A 720 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6593) covalent geometry : angle 0.72427 / 0.36 ( 8934) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.40308 / 0.24 ( 2) hydrogen bonds : bond 0.04193 / 2.99 ( 252) hydrogen bonds : angle 4.83017 / 3.31 ( 725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.203 Fit side-chains REVERT: A 313 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6600 (tt0) outliers start: 11 outliers final: 7 residues processed: 106 average time/residue: 0.0772 time to fit residues: 10.7400 Evaluate side-chains 94 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 427 CYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.212774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.190969 restraints weight = 26358.633| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 4.09 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4230 r_free = 0.4230 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4230 r_free = 0.4230 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6594 Z= 0.122 Angle : 0.616 12.553 8936 Z= 0.307 Chirality : 0.041 0.220 1023 Planarity : 0.005 0.051 1133 Dihedral : 5.292 58.010 891 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.52 % Favored : 93.23 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.30), residues: 807 helix: 1.26 (0.27), residues: 367 sheet: -0.42 (0.51), residues: 112 loop : -2.25 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.025 0.002 TYR A 489 PHE 0.011 0.001 PHE A 673 TRP 0.031 0.002 TRP A 789 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6593) covalent geometry : angle 0.61646 / 0.31 ( 8934) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.28403 / 0.17 ( 2) hydrogen bonds : bond 0.03724 / 2.56 ( 252) hydrogen bonds : angle 4.52381 / 3.11 ( 725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.237 Fit side-chains REVERT: A 313 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6999 (tt0) REVERT: A 799 ILE cc_start: 0.8323 (tp) cc_final: 0.8020 (tp) outliers start: 10 outliers final: 8 residues processed: 99 average time/residue: 0.0741 time to fit residues: 9.7961 Evaluate side-chains 97 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4340 r_free = 0.4340 target = 0.206058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182437 restraints weight = 27966.445| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 4.57 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.131 Angle : 0.664 13.481 8936 Z= 0.323 Chirality : 0.041 0.224 1023 Planarity : 0.004 0.052 1133 Dihedral : 5.348 58.519 891 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.64 % Favored : 92.11 % Rotamer: Outliers : 2.64 % Allowed : 12.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.30), residues: 807 helix: 1.21 (0.27), residues: 373 sheet: -0.41 (0.50), residues: 115 loop : -2.39 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 99 TYR 0.013 0.001 TYR A 796 PHE 0.011 0.001 PHE A 738 TRP 0.032 0.002 TRP A 789 HIS 0.004 0.001 HIS A 663 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6593) covalent geometry : angle 0.66366 / 0.32 ( 8934) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.65693 / 0.38 ( 2) hydrogen bonds : bond 0.03568 / 2.49 ( 252) hydrogen bonds : angle 4.37085 / 3.01 ( 725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.165 Fit side-chains REVERT: A 313 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 359 ASP cc_start: 0.6190 (p0) cc_final: 0.5974 (p0) REVERT: A 534 MET cc_start: 0.7810 (ptp) cc_final: 0.7392 (ptp) REVERT: A 680 ASP cc_start: 0.7955 (m-30) cc_final: 0.7689 (m-30) REVERT: A 717 GLU cc_start: 0.6556 (pm20) cc_final: 0.6327 (mt-10) REVERT: A 771 GLU cc_start: 0.7746 (tp30) cc_final: 0.7230 (tp30) REVERT: A 799 ILE cc_start: 0.8318 (tp) cc_final: 0.7948 (tp) REVERT: B 49 MET cc_start: 0.4661 (ptp) cc_final: 0.4411 (ptp) outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 0.0688 time to fit residues: 10.7145 Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.172617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144372 restraints weight = 29490.322| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 5.69 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3644 r_free = 0.3644 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 6594 Z= 0.268 Angle : 0.868 14.589 8936 Z= 0.430 Chirality : 0.048 0.209 1023 Planarity : 0.006 0.059 1133 Dihedral : 6.195 68.830 891 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.52 % Favored : 91.23 % Rotamer: Outliers : 3.47 % Allowed : 13.19 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.30), residues: 807 helix: 0.52 (0.26), residues: 387 sheet: -0.47 (0.53), residues: 112 loop : -2.62 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 836 TYR 0.009 0.002 TYR A 635 PHE 0.023 0.003 PHE A 673 TRP 0.074 0.004 TRP A 789 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.27 ( 6593) covalent geometry : angle 0.86760 / 0.43 ( 8934) SS BOND : bond 0.00202 / 0.11 ( 1) SS BOND : angle 1.22431 / 0.65 ( 2) hydrogen bonds : bond 0.05213 / 3.66 ( 252) hydrogen bonds : angle 4.87762 / 3.40 ( 725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.208 Fit side-chains REVERT: A 314 ILE cc_start: 0.7971 (tp) cc_final: 0.7551 (tt) REVERT: A 592 ARG cc_start: 0.7033 (mmt90) cc_final: 0.6795 (mpt-90) outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 0.0671 time to fit residues: 11.4246 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 : 0.171 ------------------------------------------------------------------------------- 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 678 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 789 TRP Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 841 THR 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 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN ** 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 727 ASN ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.196223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165814 restraints weight = 35608.797| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 6.73 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3936 r_free = 0.3936 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.135 Angle : 0.706 15.105 8936 Z= 0.343 Chirality : 0.041 0.223 1023 Planarity : 0.005 0.050 1133 Dihedral : 5.795 59.790 891 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.52 % Favored : 92.23 % Rotamer: Outliers : 2.22 % Allowed : 16.25 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.30), residues: 807 helix: 0.83 (0.27), residues: 388 sheet: -0.37 (0.53), residues: 105 loop : -2.49 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 99 TYR 0.018 0.002 TYR A 796 PHE 0.011 0.001 PHE A 629 TRP 0.039 0.002 TRP A 789 HIS 0.004 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 6593) covalent geometry : angle 0.70595 / 0.34 ( 8934) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.52910 / 0.29 ( 2) hydrogen bonds : bond 0.03793 / 2.63 ( 252) hydrogen bonds : angle 4.52705 / 3.17 ( 725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.150 Fit side-chains REVERT: A 314 ILE cc_start: 0.7809 (tp) cc_final: 0.7471 (tt) REVERT: A 633 MET cc_start: 0.8010 (ttm) cc_final: 0.7723 (mtp) REVERT: A 680 ASP cc_start: 0.7709 (m-30) cc_final: 0.7430 (m-30) REVERT: A 717 GLU cc_start: 0.6855 (pm20) cc_final: 0.6368 (mt-10) REVERT: B 49 MET cc_start: 0.4701 (ptp) cc_final: 0.4372 (ptp) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.0573 time to fit residues: 8.2775 Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 841 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 727 ASN ** 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 = 0.4229 r_free = 0.4229 target = 0.194555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.167293 restraints weight = 27497.481| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 5.39 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6594 Z= 0.143 Angle : 0.694 15.210 8936 Z= 0.336 Chirality : 0.042 0.227 1023 Planarity : 0.005 0.051 1133 Dihedral : 5.660 58.676 891 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.73 % Rotamer: Outliers : 2.22 % Allowed : 17.50 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.30), residues: 807 helix: 0.88 (0.27), residues: 387 sheet: -0.40 (0.53), residues: 107 loop : -2.47 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 99 TYR 0.014 0.001 TYR A 796 PHE 0.011 0.001 PHE A 673 TRP 0.024 0.002 TRP A 789 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 6593) covalent geometry : angle 0.69436 / 0.34 ( 8934) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 0.54045 / 0.29 ( 2) hydrogen bonds : bond 0.03749 / 2.61 ( 252) hydrogen bonds : angle 4.49130 / 3.14 ( 725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.145 Fit side-chains REVERT: A 314 ILE cc_start: 0.7807 (tp) cc_final: 0.7409 (tt) REVERT: A 680 ASP cc_start: 0.7739 (m-30) cc_final: 0.7471 (m-30) REVERT: A 967 MET cc_start: 0.8246 (mmm) cc_final: 0.7867 (tpp) REVERT: B 15 LEU cc_start: 0.7176 (mt) cc_final: 0.6947 (pp) REVERT: B 49 MET cc_start: 0.4650 (ptp) cc_final: 0.4306 (ptp) outliers start: 14 outliers final: 14 residues processed: 106 average time/residue: 0.0707 time to fit residues: 10.0661 Evaluate side-chains 103 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR 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 8 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 727 ASN ** 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 = 0.4224 r_free = 0.4224 target = 0.193660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162430 restraints weight = 32095.039| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 6.93 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3874 r_free = 0.3874 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5208 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= 0.172 Angle : 0.731 14.975 8936 Z= 0.356 Chirality : 0.043 0.222 1023 Planarity : 0.005 0.051 1133 Dihedral : 5.705 59.316 891 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.40 % Favored : 91.48 % Rotamer: Outliers : 2.36 % Allowed : 18.06 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.30), residues: 807 helix: 0.82 (0.27), residues: 387 sheet: -0.58 (0.53), residues: 112 loop : -2.43 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 726 TYR 0.012 0.002 TYR A 796 PHE 0.013 0.002 PHE A 673 TRP 0.030 0.002 TRP A 789 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 6593) covalent geometry : angle 0.73127 / 0.36 ( 8934) SS BOND : bond 0.00016 / 0.01 ( 1) SS BOND : angle 0.69544 / 0.37 ( 2) hydrogen bonds : bond 0.03982 / 2.78 ( 252) hydrogen bonds : angle 4.52915 / 3.16 ( 725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.219 Fit side-chains REVERT: A 314 ILE cc_start: 0.8051 (tp) cc_final: 0.7701 (tt) REVERT: A 432 GLN cc_start: 0.5913 (mm110) cc_final: 0.5447 (tt0) REVERT: A 680 ASP cc_start: 0.7728 (m-30) cc_final: 0.7470 (m-30) REVERT: A 717 GLU cc_start: 0.6956 (pm20) cc_final: 0.6444 (mt-10) REVERT: B 15 LEU cc_start: 0.7169 (mt) cc_final: 0.6931 (pp) outliers start: 15 outliers final: 15 residues processed: 105 average time/residue: 0.0593 time to fit residues: 8.3529 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 : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR 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 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 727 ASN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.195489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167376 restraints weight = 32562.240| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 5.92 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3948 r_free = 0.3948 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 = 0.3948 r_free = 0.3948 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.126 Angle : 0.686 15.522 8936 Z= 0.333 Chirality : 0.041 0.227 1023 Planarity : 0.004 0.050 1133 Dihedral : 5.562 57.965 891 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 2.08 % Allowed : 18.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.30), residues: 807 helix: 0.96 (0.27), residues: 388 sheet: -0.47 (0.53), residues: 107 loop : -2.45 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 99 TYR 0.016 0.001 TYR A 796 PHE 0.013 0.001 PHE A 629 TRP 0.018 0.001 TRP A 789 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6593) covalent geometry : angle 0.68614 / 0.33 ( 8934) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 0.42238 / 0.23 ( 2) hydrogen bonds : bond 0.03480 / 2.42 ( 252) hydrogen bonds : angle 4.43044 / 3.09 ( 725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.144 Fit side-chains REVERT: A 314 ILE cc_start: 0.7941 (tp) cc_final: 0.7564 (tt) REVERT: A 432 GLN cc_start: 0.5806 (mm110) cc_final: 0.5374 (tt0) REVERT: A 680 ASP cc_start: 0.7448 (m-30) cc_final: 0.7142 (m-30) REVERT: A 717 GLU cc_start: 0.6882 (pm20) cc_final: 0.6382 (mt-10) outliers start: 13 outliers final: 12 residues processed: 106 average time/residue: 0.0575 time to fit residues: 8.4151 Evaluate side-chains 106 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 727 ASN Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.0000 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 61 optimal weight: 0.0270 chunk 41 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4270 r_free = 0.4270 target = 0.198593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.176296 restraints weight = 22907.946| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.78 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6594 Z= 0.121 Angle : 0.687 15.764 8936 Z= 0.333 Chirality : 0.040 0.224 1023 Planarity : 0.004 0.050 1133 Dihedral : 5.429 58.018 891 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.89 % Favored : 91.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.30), residues: 807 helix: 1.06 (0.27), residues: 388 sheet: -0.42 (0.53), residues: 107 loop : -2.37 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 99 TYR 0.017 0.001 TYR A 796 PHE 0.007 0.001 PHE A 787 TRP 0.016 0.001 TRP A 789 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6593) covalent geometry : angle 0.68744 / 0.33 ( 8934) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.29684 / 0.16 ( 2) hydrogen bonds : bond 0.03299 / 2.27 ( 252) hydrogen bonds : angle 4.38213 / 3.05 ( 725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.227 Fit side-chains REVERT: A 314 ILE cc_start: 0.7909 (tp) cc_final: 0.7587 (tt) REVERT: A 432 GLN cc_start: 0.5636 (mm110) cc_final: 0.5311 (tt0) REVERT: A 680 ASP cc_start: 0.7332 (m-30) cc_final: 0.7066 (m-30) REVERT: A 717 GLU cc_start: 0.6656 (pm20) cc_final: 0.6402 (mt-10) REVERT: A 967 MET cc_start: 0.7675 (mmm) cc_final: 0.7311 (tpp) outliers start: 12 outliers final: 11 residues processed: 107 average time/residue: 0.0699 time to fit residues: 10.2592 Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4232 r_free = 0.4232 target = 0.195120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172321 restraints weight = 24988.870| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.91 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4016 r_free = 0.4016 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 = 0.4016 r_free = 0.4016 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6594 Z= 0.139 Angle : 0.705 15.391 8936 Z= 0.343 Chirality : 0.041 0.216 1023 Planarity : 0.004 0.048 1133 Dihedral : 5.509 56.645 891 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.02 % Favored : 91.85 % Rotamer: Outliers : 1.81 % Allowed : 19.17 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.30), residues: 807 helix: 0.98 (0.27), residues: 388 sheet: -0.41 (0.53), residues: 107 loop : -2.35 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 99 TYR 0.013 0.001 TYR A 796 PHE 0.012 0.001 PHE A 629 TRP 0.023 0.001 TRP A 789 HIS 0.004 0.001 HIS B 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6593) covalent geometry : angle 0.70455 / 0.34 ( 8934) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.45371 / 0.24 ( 2) hydrogen bonds : bond 0.03482 / 2.40 ( 252) hydrogen bonds : angle 4.45713 / 3.10 ( 725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.84 seconds wall clock time: 19 minutes 29.01 seconds (1169.01 seconds total)