Starting phenix.real_space_refine on Wed Mar 4 09:18:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kx9_23063/03_2026/7kx9_23063.map" } resolution = 3.5 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= 0.003 sd= 0.033 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 25 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: 7 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 4015 2.51 5 N 1170 2.21 5 O 1318 1.98 5 H 5846 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 11133 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 38, 'TRANS': 695} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 774 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 515 Classifications: {'RNA': 16} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.19 Number of scatterers: 12424 At special positions: 0 Unit cell: (79.35, 109.25, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 P 40 15.00 Mg 2 11.99 O 1318 8.00 N 1170 7.00 C 4015 6.00 H 5846 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 330.4 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 33.9% alpha, 16.2% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 347 removed outlier: 3.708A pdb=" N ARG A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 528 through 539 removed outlier: 3.641A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.551A pdb=" N SER A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 692 through 705 Processing helix chain 'A' and resid 717 through 721 removed outlier: 4.297A pdb=" N GLN A 721 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.560A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 819 Processing helix chain 'A' and resid 836 through 851 removed outlier: 4.021A pdb=" N VAL A 840 " --> pdb=" O ARG A 836 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix removed outlier: 3.883A pdb=" N CYS A 851 " --> pdb=" O GLN A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.616A pdb=" N PHE A 855 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 955 through 969 removed outlier: 3.651A pdb=" N ASN A 959 " --> pdb=" O PRO A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.804A pdb=" N LEU A 578 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.439A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 390 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 379 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 392 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 373 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 376 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 357 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.504A pdb=" N VAL A 287 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 322 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 441 removed outlier: 3.512A pdb=" N ARG A 438 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 456 Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.678A pdb=" N ALA A 746 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 660 through 661 removed outlier: 7.529A pdb=" N VAL A 661 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 627 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 626 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 684 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU A 714 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 686 " --> pdb=" O LEU A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.957A pdb=" N MET A 755 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE A 828 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 757 " --> pdb=" O PHE A 828 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A 863 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 925 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 865 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 923 " --> pdb=" O VAL A 865 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5834 1.03 - 1.23: 40 1.23 - 1.42: 2910 1.42 - 1.61: 3808 1.61 - 1.81: 54 Bond restraints: 12646 Sorted by residual: bond pdb=" C2 OMG B 24 " pdb=" N3 OMG B 24 " ideal model delta sigma weight residual 1.308 1.478 -0.170 2.00e-02 2.50e+03 7.27e+01 bond pdb=" N3 OMG B 24 " pdb=" C4 OMG B 24 " ideal model delta sigma weight residual 1.341 1.493 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C2 OMG B 24 " pdb=" N2 OMG B 24 " ideal model delta sigma weight residual 1.344 1.487 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C5 OMG B 24 " pdb=" C6 OMG B 24 " ideal model delta sigma weight residual 1.424 1.544 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N1 OMG B 24 " pdb=" C2 OMG B 24 " ideal model delta sigma weight residual 1.365 1.439 -0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 22689 5.48 - 10.96: 13 10.96 - 16.44: 0 16.44 - 21.92: 0 21.92 - 27.40: 4 Bond angle restraints: 22706 Sorted by residual: angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP1 U B 11 " ideal model delta sigma weight residual 108.00 80.60 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C8 OMG B 24 " ideal model delta sigma weight residual 127.59 100.49 27.10 3.00e+00 1.11e-01 8.16e+01 angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C4 OMG B 24 " ideal model delta sigma weight residual 125.50 151.60 -26.10 3.00e+00 1.11e-01 7.57e+01 angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 108.00 83.25 24.75 3.00e+00 1.11e-01 6.80e+01 angle pdb=" OP1 U B 11 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 119.60 130.39 -10.79 3.00e+00 1.11e-01 1.29e+01 ... (remaining 22701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 5570 24.09 - 48.19: 330 48.19 - 72.28: 87 72.28 - 96.37: 19 96.37 - 120.47: 4 Dihedral angle restraints: 6010 sinusoidal: 3505 harmonic: 2505 Sorted by residual: dihedral pdb=" CA ARG A 286 " pdb=" C ARG A 286 " pdb=" N VAL A 287 " pdb=" CA VAL A 287 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 850 " pdb=" C SER A 850 " pdb=" N CYS A 851 " pdb=" CA CYS A 851 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 895 " pdb=" C HIS A 895 " pdb=" N THR A 896 " pdb=" CA THR A 896 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 1088 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.921: 1 Chirality restraints: 1089 Sorted by residual: chirality pdb=" P U B 11 " pdb=" OP1 U B 11 " pdb=" OP2 U B 11 " pdb=" O5' U B 11 " both_signs ideal model delta sigma weight residual True 2.41 0.49 1.92 2.00e-01 2.50e+01 9.22e+01 chirality pdb=" C1' G C 22 " pdb=" O4' G C 22 " pdb=" C2' G C 22 " pdb=" N9 G C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET A 398 " pdb=" N MET A 398 " pdb=" C MET A 398 " pdb=" CB MET A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1086 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 860 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 861 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 861 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 861 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 397 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 397 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 397 " -0.010 2.00e-02 2.50e+03 pdb=" N MET A 398 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 22 " 0.019 2.00e-02 2.50e+03 8.46e-03 2.50e+00 pdb=" N9 G C 22 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G C 22 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 22 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 22 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 22 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G C 22 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" H8 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" H1 G C 22 " 0.000 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 52 1.86 - 2.54: 10717 2.54 - 3.23: 36642 3.23 - 3.91: 45816 3.91 - 4.60: 73739 Nonbonded interactions: 166966 Sorted by model distance: nonbonded pdb="HH21 ARG A 953 " pdb=" OP2 U B 6 " model vdw 1.172 2.450 nonbonded pdb=" HD1 HIS A 962 " pdb="MG MG A1002 " model vdw 1.466 1.700 nonbonded pdb=" HE2 TYR A 468 " pdb=" H3' OMG B 24 " model vdw 1.497 2.270 nonbonded pdb="HE22 GLN A 735 " pdb="MG MG A1001 " model vdw 1.547 1.700 nonbonded pdb=" O ASN A 663 " pdb=" HG SER A 668 " model vdw 1.548 2.450 ... (remaining 166961 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.012 0.790 6801 Z= 1.025 Angle : 0.934 27.403 9412 Z= 0.453 Chirality : 0.074 1.921 1089 Planarity : 0.005 0.044 1062 Dihedral : 17.248 120.468 2747 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.70 (0.30), residues: 728 helix: -0.96 (0.34), residues: 224 sheet: -3.45 (0.34), residues: 187 loop : -2.83 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 629 TYR 0.011 0.002 TYR A 435 PHE 0.009 0.001 PHE A 340 TRP 0.006 0.001 TRP A 623 HIS 0.009 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 6800) covalent geometry : angle 0.93373 ( 9412) hydrogen bonds : bond 0.23118 ( 241) hydrogen bonds : angle 8.95913 ( 650) Misc. bond : bond 0.79026 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8702 (mt) cc_final: 0.8457 (mt) REVERT: A 908 GLN cc_start: 0.7761 (tp40) cc_final: 0.7422 (tp40) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.2108 time to fit residues: 23.2147 Evaluate side-chains 68 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102535 restraints weight = 26281.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108571 restraints weight = 12509.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112359 restraints weight = 8295.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114649 restraints weight = 6493.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115923 restraints weight = 5591.155| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6801 Z= 0.176 Angle : 0.760 27.298 9412 Z= 0.356 Chirality : 0.072 1.893 1089 Planarity : 0.005 0.087 1062 Dihedral : 17.593 116.522 1402 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.96 (0.30), residues: 728 helix: -0.06 (0.34), residues: 220 sheet: -2.96 (0.37), residues: 171 loop : -2.71 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 671 TYR 0.013 0.001 TYR A 376 PHE 0.019 0.001 PHE A 406 TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6800) covalent geometry : angle 0.76003 ( 9412) hydrogen bonds : bond 0.05782 ( 241) hydrogen bonds : angle 6.31648 ( 650) Misc. bond : bond 0.00447 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7322 (mmp) cc_final: 0.6804 (mmp) REVERT: A 621 LEU cc_start: 0.8719 (mt) cc_final: 0.8480 (mt) REVERT: A 793 GLN cc_start: 0.6627 (mp10) cc_final: 0.4471 (mp10) REVERT: A 812 LYS cc_start: 0.8708 (tppt) cc_final: 0.8486 (tppt) REVERT: A 908 GLN cc_start: 0.7593 (tp40) cc_final: 0.7306 (tp40) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1978 time to fit residues: 19.2288 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 50.0000 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.0270 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** 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 = 0.3874 r_free = 0.3874 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102472 restraints weight = 26850.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108659 restraints weight = 12730.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112518 restraints weight = 8404.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114721 restraints weight = 6564.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116219 restraints weight = 5673.359| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6801 Z= 0.141 Angle : 0.694 26.836 9412 Z= 0.321 Chirality : 0.072 1.926 1089 Planarity : 0.004 0.054 1062 Dihedral : 17.478 125.486 1400 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.17 % Allowed : 6.67 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.47 (0.31), residues: 728 helix: 0.51 (0.36), residues: 221 sheet: -2.74 (0.37), residues: 171 loop : -2.52 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.010 0.001 TYR A 376 PHE 0.013 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.010 0.001 HIS A 763 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6800) covalent geometry : angle 0.69380 ( 9412) hydrogen bonds : bond 0.04596 ( 241) hydrogen bonds : angle 5.65305 ( 650) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8755 (mt) cc_final: 0.8508 (mt) REVERT: A 812 LYS cc_start: 0.8777 (tppt) cc_final: 0.8452 (tppt) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.2162 time to fit residues: 21.4516 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 61 optimal weight: 0.0980 chunk 54 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 22 optimal weight: 50.0000 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.145699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101370 restraints weight = 26344.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107403 restraints weight = 12541.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111230 restraints weight = 8304.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113481 restraints weight = 6496.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114763 restraints weight = 5600.132| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6801 Z= 0.177 Angle : 0.696 26.998 9412 Z= 0.321 Chirality : 0.072 1.918 1089 Planarity : 0.004 0.049 1062 Dihedral : 17.442 125.950 1400 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.83 % Allowed : 7.50 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.31), residues: 728 helix: 0.65 (0.35), residues: 222 sheet: -2.63 (0.37), residues: 173 loop : -2.42 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.011 0.001 TYR A 376 PHE 0.014 0.001 PHE A 340 TRP 0.007 0.001 TRP A 569 HIS 0.009 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6800) covalent geometry : angle 0.69554 ( 9412) hydrogen bonds : bond 0.04212 ( 241) hydrogen bonds : angle 5.37097 ( 650) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8763 (mt) cc_final: 0.8541 (mt) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.2175 time to fit residues: 20.1298 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 793 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 0.0010 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100768 restraints weight = 26802.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106947 restraints weight = 12786.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110742 restraints weight = 8442.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113075 restraints weight = 6606.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114460 restraints weight = 5682.971| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6801 Z= 0.170 Angle : 0.684 26.964 9412 Z= 0.315 Chirality : 0.072 1.925 1089 Planarity : 0.004 0.045 1062 Dihedral : 17.425 129.509 1400 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.17 % Allowed : 8.00 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.32), residues: 728 helix: 0.83 (0.36), residues: 222 sheet: -2.54 (0.38), residues: 171 loop : -2.38 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.010 0.001 TYR A 376 PHE 0.014 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6800) covalent geometry : angle 0.68359 ( 9412) hydrogen bonds : bond 0.03955 ( 241) hydrogen bonds : angle 5.25029 ( 650) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8792 (mt) cc_final: 0.8577 (mt) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2096 time to fit residues: 19.9723 Evaluate side-chains 73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.145883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101231 restraints weight = 26823.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107395 restraints weight = 12826.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111240 restraints weight = 8500.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113585 restraints weight = 6645.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115054 restraints weight = 5715.767| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6801 Z= 0.144 Angle : 0.675 26.907 9412 Z= 0.309 Chirality : 0.072 1.936 1089 Planarity : 0.004 0.043 1062 Dihedral : 17.365 130.722 1400 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.83 % Allowed : 9.33 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.32), residues: 728 helix: 0.92 (0.36), residues: 228 sheet: -2.43 (0.38), residues: 171 loop : -2.33 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 936 TYR 0.010 0.001 TYR A 376 PHE 0.012 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6800) covalent geometry : angle 0.67471 ( 9412) hydrogen bonds : bond 0.03824 ( 241) hydrogen bonds : angle 5.10155 ( 650) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8829 (mt) cc_final: 0.8611 (mt) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.2292 time to fit residues: 20.6178 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 793 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099506 restraints weight = 26491.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105519 restraints weight = 12852.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109246 restraints weight = 8536.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111481 restraints weight = 6691.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112462 restraints weight = 5782.985| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6801 Z= 0.205 Angle : 0.693 27.097 9412 Z= 0.321 Chirality : 0.072 1.927 1089 Planarity : 0.004 0.043 1062 Dihedral : 17.383 132.996 1400 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.33 % Allowed : 10.33 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.32), residues: 728 helix: 0.86 (0.35), residues: 228 sheet: -2.43 (0.38), residues: 173 loop : -2.37 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.011 0.001 TYR A 357 PHE 0.015 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6800) covalent geometry : angle 0.69279 ( 9412) hydrogen bonds : bond 0.03951 ( 241) hydrogen bonds : angle 5.14392 ( 650) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7505 (mmp) cc_final: 0.6717 (mmp) REVERT: A 621 LEU cc_start: 0.8833 (mt) cc_final: 0.8632 (mt) REVERT: A 802 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6362 (mt-10) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.2349 time to fit residues: 20.6867 Evaluate side-chains 74 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 793 GLN Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** 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 = 0.3851 r_free = 0.3851 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100779 restraints weight = 26101.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106725 restraints weight = 12432.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110425 restraints weight = 8209.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112684 restraints weight = 6429.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114101 restraints weight = 5540.574| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6801 Z= 0.158 Angle : 0.676 26.973 9412 Z= 0.311 Chirality : 0.072 1.936 1089 Planarity : 0.004 0.043 1062 Dihedral : 17.307 134.271 1400 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.33 % Allowed : 11.00 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.32), residues: 728 helix: 0.93 (0.36), residues: 230 sheet: -2.37 (0.38), residues: 173 loop : -2.29 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.010 0.001 TYR A 376 PHE 0.013 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6800) covalent geometry : angle 0.67595 ( 9412) hydrogen bonds : bond 0.03744 ( 241) hydrogen bonds : angle 5.02105 ( 650) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7488 (mmp) cc_final: 0.6708 (mmp) REVERT: A 802 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6222 (mt-10) outliers start: 8 outliers final: 8 residues processed: 70 average time/residue: 0.2202 time to fit residues: 19.6248 Evaluate side-chains 73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 793 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098515 restraints weight = 26686.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104385 restraints weight = 12870.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108023 restraints weight = 8581.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110324 restraints weight = 6749.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111616 restraints weight = 5808.429| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6801 Z= 0.231 Angle : 0.709 27.119 9412 Z= 0.329 Chirality : 0.072 1.923 1089 Planarity : 0.004 0.043 1062 Dihedral : 17.357 136.346 1400 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 1.50 % Allowed : 11.00 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.09 (0.32), residues: 728 helix: 0.75 (0.35), residues: 230 sheet: -2.41 (0.39), residues: 174 loop : -2.36 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 879 TYR 0.011 0.001 TYR A 357 PHE 0.017 0.001 PHE A 340 TRP 0.008 0.001 TRP A 605 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 6800) covalent geometry : angle 0.70918 ( 9412) hydrogen bonds : bond 0.03962 ( 241) hydrogen bonds : angle 5.12554 ( 650) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6274 (mt-10) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.2378 time to fit residues: 20.1272 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 793 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.147440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103204 restraints weight = 26383.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109427 restraints weight = 12423.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113325 restraints weight = 8107.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115763 restraints weight = 6272.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116925 restraints weight = 5346.576| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6801 Z= 0.092 Angle : 0.661 26.725 9412 Z= 0.302 Chirality : 0.072 1.959 1089 Planarity : 0.004 0.043 1062 Dihedral : 17.160 137.842 1400 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.00 % Allowed : 11.67 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.33), residues: 728 helix: 1.21 (0.36), residues: 231 sheet: -2.02 (0.40), residues: 174 loop : -2.21 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 936 TYR 0.009 0.001 TYR A 357 PHE 0.009 0.001 PHE A 966 TRP 0.008 0.001 TRP A 569 HIS 0.003 0.001 HIS A 943 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 6800) covalent geometry : angle 0.66127 ( 9412) hydrogen bonds : bond 0.03413 ( 241) hydrogen bonds : angle 4.81901 ( 650) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7505 (mmt) cc_final: 0.6715 (mmp) REVERT: A 802 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6269 (mt-10) outliers start: 6 outliers final: 6 residues processed: 74 average time/residue: 0.2177 time to fit residues: 20.2934 Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 793 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 0.0050 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100702 restraints weight = 26579.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106720 restraints weight = 12771.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110464 restraints weight = 8501.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112716 restraints weight = 6683.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114138 restraints weight = 5776.610| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6801 Z= 0.155 Angle : 0.665 26.973 9412 Z= 0.303 Chirality : 0.072 1.947 1089 Planarity : 0.004 0.038 1062 Dihedral : 17.166 139.301 1400 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.17 % Allowed : 11.83 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.33), residues: 728 helix: 1.16 (0.36), residues: 231 sheet: -2.00 (0.40), residues: 174 loop : -2.19 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 396 TYR 0.011 0.001 TYR A 357 PHE 0.007 0.001 PHE A 406 TRP 0.007 0.001 TRP A 569 HIS 0.003 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6800) covalent geometry : angle 0.66460 ( 9412) hydrogen bonds : bond 0.03556 ( 241) hydrogen bonds : angle 4.86483 ( 650) Misc. bond : bond 0.00047 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.68 seconds wall clock time: 37 minutes 16.90 seconds (2236.90 seconds total)