Starting phenix.real_space_refine on Thu Jul 2 02:59:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kx7_23061/07_2026/7kx7_23061.map" } resolution = 3.8 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= 0.001 sd= 0.028 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 82 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 7 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 3676 2.51 5 N 1035 2.21 5 O 1075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s 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: 5828 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5679 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 38, 'TRANS': 690} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 4, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Classifications: {'RNA': 7} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 1.47, per 1000 atoms: 0.25 Number of scatterers: 5828 At special positions: 0 Unit cell: (78.2, 103.5, 79.35, 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 33 16.00 P 7 15.00 Mg 2 11.99 O 1075 8.00 N 1035 7.00 C 3676 6.00 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=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 458.8 milliseconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 10 sheets defined 32.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 267 through 277 removed outlier: 4.030A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 330 through 347 removed outlier: 4.452A pdb=" N GLN A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 338 " --> pdb=" O GLN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 4.100A pdb=" N GLU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 528 through 539 removed outlier: 4.204A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.646A pdb=" N GLU A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.691A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.668A pdb=" N LYS A 611 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 631 through 650 removed outlier: 3.795A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Proline residue: A 647 - end of helix Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.542A pdb=" N TYR A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 705 removed outlier: 3.835A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 725 through 740 removed outlier: 3.805A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 819 removed outlier: 3.656A pdb=" N LEU A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 5.836A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix removed outlier: 3.828A pdb=" N PHE A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 930 through 941 Processing helix chain 'A' and resid 955 through 971 Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.532A pdb=" N SER A 981 " --> pdb=" O HIS A 978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 786 through 791 removed outlier: 3.605A pdb=" N ALA A 773 " --> pdb=" O ALA A 791 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 772 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 760 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL A 756 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A 863 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP A 925 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 865 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 891 " --> pdb=" O VAL A 906 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 240 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.781A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 355 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.781A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 388 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 381 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.621A pdb=" N ASP A 325 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 308 Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.548A pdb=" N ILE A 463 " --> pdb=" O PHE A 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB1, first strand: chain 'A' and resid 657 through 660 removed outlier: 5.402A pdb=" N VAL A 625 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU A 626 " --> pdb=" O VAL A 687 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 937 1.32 - 1.44: 1594 1.44 - 1.57: 3365 1.57 - 1.69: 12 1.69 - 1.82: 54 Bond restraints: 5962 Sorted by residual: bond pdb=" C5 OMC B 25 " pdb=" C6 OMC B 25 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C2 OMC B 25 " pdb=" N3 OMC B 25 " ideal model delta sigma weight residual 1.350 1.484 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" N3 OMC B 25 " pdb=" C4 OMC B 25 " ideal model delta sigma weight residual 1.317 1.448 -0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C4 OMC B 25 " pdb=" N4 OMC B 25 " ideal model delta sigma weight residual 1.332 1.436 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" N1 OMC B 25 " pdb=" C6 OMC B 25 " ideal model delta sigma weight residual 1.357 1.448 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 5957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 7645 1.51 - 3.02: 385 3.02 - 4.53: 65 4.53 - 6.04: 14 6.04 - 7.55: 3 Bond angle restraints: 8112 Sorted by residual: angle pdb=" N GLN A 721 " pdb=" CA GLN A 721 " pdb=" C GLN A 721 " ideal model delta sigma weight residual 113.23 108.30 4.93 1.22e+00 6.72e-01 1.63e+01 angle pdb=" CA LYS A 899 " pdb=" C LYS A 899 " pdb=" O LYS A 899 " ideal model delta sigma weight residual 121.44 117.00 4.44 1.17e+00 7.31e-01 1.44e+01 angle pdb=" CA ILE A 299 " pdb=" C ILE A 299 " pdb=" O ILE A 299 " ideal model delta sigma weight residual 122.13 118.05 4.08 1.11e+00 8.12e-01 1.35e+01 angle pdb=" N GLN A 722 " pdb=" CA GLN A 722 " pdb=" C GLN A 722 " ideal model delta sigma weight residual 112.72 108.37 4.35 1.28e+00 6.10e-01 1.16e+01 angle pdb=" CA ASP A 902 " pdb=" C ASP A 902 " pdb=" O ASP A 902 " ideal model delta sigma weight residual 121.44 117.52 3.92 1.17e+00 7.31e-01 1.12e+01 ... (remaining 8107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 3268 17.39 - 34.78: 281 34.78 - 52.16: 31 52.16 - 69.55: 9 69.55 - 86.94: 8 Dihedral angle restraints: 3597 sinusoidal: 1455 harmonic: 2142 Sorted by residual: dihedral pdb=" CA ASN A 262 " pdb=" C ASN A 262 " pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP A 325 " pdb=" C ASP A 325 " pdb=" N SER A 326 " pdb=" CA SER A 326 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PRO A 512 " pdb=" C PRO A 512 " pdb=" N GLU A 513 " pdb=" CA GLU A 513 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 3594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 714 0.058 - 0.116: 182 0.116 - 0.174: 17 0.174 - 0.232: 5 0.232 - 0.290: 3 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA ILE A 897 " pdb=" N ILE A 897 " pdb=" C ILE A 897 " pdb=" CB ILE A 897 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 262 " pdb=" N ASN A 262 " pdb=" C ASN A 262 " pdb=" CB ASN A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 918 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 522 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C ASP A 522 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP A 522 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 647 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 648 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 648 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 648 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 859 " -0.016 2.00e-02 2.50e+03 1.35e-02 3.65e+00 pdb=" CG TYR A 859 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 859 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 859 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 859 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 859 " -0.001 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 60 2.54 - 3.13: 4690 3.13 - 3.72: 8780 3.72 - 4.31: 11862 4.31 - 4.90: 20306 Nonbonded interactions: 45698 Sorted by model distance: nonbonded pdb=" OP1 U B 3 " pdb="MG MG A1001 " model vdw 1.953 2.170 nonbonded pdb=" OXT LEU A 987 " pdb="MG MG A1001 " model vdw 1.963 2.170 nonbonded pdb=" O LEU A 987 " pdb="MG MG A1001 " model vdw 1.997 2.170 nonbonded pdb=" NH2 ARG A 583 " pdb=" OE1 GLN A 935 " model vdw 2.201 3.120 nonbonded pdb=" OE1 GLU A 364 " pdb=" NE2 GLN A 371 " model vdw 2.221 3.120 ... (remaining 45693 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: 0.060 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.030 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.007 0.137 5962 Z= 0.362 Angle : 0.786 7.550 8112 Z= 0.464 Chirality : 0.052 0.290 921 Planarity : 0.004 0.050 1018 Dihedral : 13.234 86.937 2209 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.17 % Allowed : 0.67 % Favored : 99.16 % 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: -2.63 (0.31), residues: 721 helix: -0.03 (0.38), residues: 199 sheet: -2.35 (0.41), residues: 147 loop : -2.50 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 607 TYR 0.032 0.002 TYR A 859 PHE 0.013 0.002 PHE A 852 TRP 0.019 0.002 TRP A 373 HIS 0.006 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.36 ( 5962) covalent geometry : angle 0.78647 / 0.46 ( 8112) hydrogen bonds : bond 0.21224 / 15.39 ( 212) hydrogen bonds : angle 9.63613 / 6.82 ( 621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 517 MET cc_start: 0.7805 (mpp) cc_final: 0.7497 (mpp) REVERT: A 743 GLU cc_start: 0.8404 (pm20) cc_final: 0.7992 (pt0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0714 time to fit residues: 8.1628 Evaluate side-chains 68 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 663 ASN A 712 GLN A 722 GLN A 735 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091766 restraints weight = 10756.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.092056 restraints weight = 7232.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092962 restraints weight = 5916.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093203 restraints weight = 5204.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095147 restraints weight = 4853.489| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5962 Z= 0.179 Angle : 0.613 8.266 8112 Z= 0.318 Chirality : 0.046 0.224 921 Planarity : 0.005 0.047 1018 Dihedral : 6.064 56.369 872 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.85 % Allowed : 8.72 % Favored : 89.43 % 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: -2.18 (0.32), residues: 721 helix: 0.70 (0.39), residues: 200 sheet: -2.23 (0.39), residues: 143 loop : -2.40 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 665 TYR 0.028 0.002 TYR A 859 PHE 0.030 0.002 PHE A 528 TRP 0.008 0.001 TRP A 373 HIS 0.006 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 5962) covalent geometry : angle 0.61329 / 0.32 ( 8112) hydrogen bonds : bond 0.04486 / 3.15 ( 212) hydrogen bonds : angle 6.70444 / 4.81 ( 621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.162 Fit side-chains REVERT: A 465 PHE cc_start: 0.8733 (m-80) cc_final: 0.8379 (m-80) REVERT: A 517 MET cc_start: 0.7704 (mpp) cc_final: 0.7478 (mpp) REVERT: A 680 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6885 (tmm160) outliers start: 11 outliers final: 4 residues processed: 84 average time/residue: 0.0589 time to fit residues: 6.9336 Evaluate side-chains 72 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 772 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.090119 restraints weight = 10762.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.090507 restraints weight = 7366.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.091622 restraints weight = 6147.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092027 restraints weight = 5120.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.092320 restraints weight = 4814.114| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5962 Z= 0.239 Angle : 0.609 9.234 8112 Z= 0.316 Chirality : 0.046 0.238 921 Planarity : 0.004 0.048 1018 Dihedral : 5.937 55.536 872 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.35 % Allowed : 11.91 % Favored : 85.74 % 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: -2.04 (0.32), residues: 721 helix: 0.85 (0.39), residues: 202 sheet: -2.19 (0.39), residues: 141 loop : -2.32 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 607 TYR 0.018 0.002 TYR A 859 PHE 0.026 0.002 PHE A 528 TRP 0.009 0.002 TRP A 623 HIS 0.006 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 ( 5962) covalent geometry : angle 0.60911 / 0.32 ( 8112) hydrogen bonds : bond 0.04277 / 3.03 ( 212) hydrogen bonds : angle 6.20320 / 4.46 ( 621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.239 Fit side-chains REVERT: A 465 PHE cc_start: 0.8673 (m-80) cc_final: 0.8301 (m-80) REVERT: A 517 MET cc_start: 0.7834 (mpp) cc_final: 0.7610 (mpp) REVERT: A 573 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8089 (mp) REVERT: A 605 TRP cc_start: 0.8906 (p90) cc_final: 0.8585 (p90) outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 0.0642 time to fit residues: 6.7201 Evaluate side-chains 75 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090373 restraints weight = 10830.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.090808 restraints weight = 7411.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092001 restraints weight = 6144.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092370 restraints weight = 5080.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092621 restraints weight = 4801.156| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5962 Z= 0.218 Angle : 0.592 7.610 8112 Z= 0.308 Chirality : 0.046 0.208 921 Planarity : 0.004 0.048 1018 Dihedral : 5.893 55.100 872 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.85 % Allowed : 13.26 % Favored : 84.90 % 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: -2.01 (0.32), residues: 721 helix: 0.88 (0.39), residues: 202 sheet: -2.19 (0.38), residues: 142 loop : -2.30 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 607 TYR 0.015 0.002 TYR A 859 PHE 0.015 0.002 PHE A 406 TRP 0.008 0.002 TRP A 623 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 5962) covalent geometry : angle 0.59167 / 0.31 ( 8112) hydrogen bonds : bond 0.03934 / 2.76 ( 212) hydrogen bonds : angle 5.96896 / 4.29 ( 621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.191 Fit side-chains REVERT: A 465 PHE cc_start: 0.8658 (m-80) cc_final: 0.8269 (m-80) REVERT: A 517 MET cc_start: 0.7830 (mpp) cc_final: 0.7624 (mpp) REVERT: A 605 TRP cc_start: 0.8912 (p90) cc_final: 0.8615 (p90) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.0598 time to fit residues: 6.0057 Evaluate side-chains 71 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 693 ASP Chi-restraints excluded: chain A residue 699 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.0170 overall best weight: 2.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 ASN A 793 GLN A 959 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093810 restraints weight = 10766.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094329 restraints weight = 7113.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095497 restraints weight = 5830.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095825 restraints weight = 4894.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.096158 restraints weight = 4578.506| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5962 Z= 0.115 Angle : 0.541 9.078 8112 Z= 0.277 Chirality : 0.044 0.172 921 Planarity : 0.004 0.050 1018 Dihedral : 5.510 52.764 872 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.68 % Allowed : 14.77 % Favored : 83.56 % 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: -1.68 (0.32), residues: 721 helix: 1.23 (0.40), residues: 199 sheet: -2.27 (0.39), residues: 133 loop : -2.00 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.018 0.001 TYR A 244 PHE 0.018 0.001 PHE A 528 TRP 0.008 0.001 TRP A 623 HIS 0.003 0.000 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 5962) covalent geometry : angle 0.54120 / 0.28 ( 8112) hydrogen bonds : bond 0.03307 / 2.27 ( 212) hydrogen bonds : angle 5.46697 / 3.88 ( 621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8675 (m-80) cc_final: 0.8201 (m-80) outliers start: 10 outliers final: 4 residues processed: 86 average time/residue: 0.0640 time to fit residues: 7.5435 Evaluate side-chains 77 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092052 restraints weight = 10708.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092200 restraints weight = 7821.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093445 restraints weight = 6727.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093785 restraints weight = 5468.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.094101 restraints weight = 5182.341| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5962 Z= 0.211 Angle : 0.617 15.175 8112 Z= 0.309 Chirality : 0.045 0.177 921 Planarity : 0.004 0.047 1018 Dihedral : 5.541 52.327 872 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.01 % Allowed : 15.94 % Favored : 82.05 % 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: -1.69 (0.32), residues: 721 helix: 1.19 (0.39), residues: 199 sheet: -2.32 (0.39), residues: 137 loop : -1.97 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.020 0.002 TYR A 859 PHE 0.013 0.002 PHE A 406 TRP 0.033 0.002 TRP A 605 HIS 0.009 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 5962) covalent geometry : angle 0.61656 / 0.31 ( 8112) hydrogen bonds : bond 0.03521 / 2.44 ( 212) hydrogen bonds : angle 5.42136 / 3.86 ( 621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8576 (m-80) cc_final: 0.8117 (m-80) REVERT: A 658 MET cc_start: 0.8519 (tpp) cc_final: 0.8275 (tmm) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.0671 time to fit residues: 7.4758 Evaluate side-chains 78 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093288 restraints weight = 10634.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094154 restraints weight = 6989.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096295 restraints weight = 5413.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096232 restraints weight = 4381.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096417 restraints weight = 4203.482| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5962 Z= 0.145 Angle : 0.584 13.896 8112 Z= 0.293 Chirality : 0.044 0.166 921 Planarity : 0.004 0.047 1018 Dihedral : 5.446 51.786 872 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.01 % Allowed : 15.44 % Favored : 82.55 % 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: -1.66 (0.32), residues: 721 helix: 1.23 (0.39), residues: 199 sheet: -2.22 (0.40), residues: 135 loop : -1.99 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.022 0.002 TYR A 859 PHE 0.031 0.002 PHE A 852 TRP 0.017 0.001 TRP A 605 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 5962) covalent geometry : angle 0.58418 / 0.29 ( 8112) hydrogen bonds : bond 0.03295 / 2.26 ( 212) hydrogen bonds : angle 5.28806 / 3.76 ( 621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 449 LYS cc_start: 0.8065 (pttt) cc_final: 0.7858 (pttm) REVERT: A 465 PHE cc_start: 0.8692 (m-80) cc_final: 0.8146 (m-80) REVERT: A 658 MET cc_start: 0.8531 (tpp) cc_final: 0.8287 (tmm) REVERT: A 680 ARG cc_start: 0.7364 (tmm160) cc_final: 0.7122 (tmm160) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.0646 time to fit residues: 7.1957 Evaluate side-chains 79 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.120563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091930 restraints weight = 10708.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092346 restraints weight = 7236.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093596 restraints weight = 6020.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093775 restraints weight = 4955.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095376 restraints weight = 4684.668| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5962 Z= 0.185 Angle : 0.597 13.347 8112 Z= 0.300 Chirality : 0.045 0.163 921 Planarity : 0.004 0.046 1018 Dihedral : 5.454 51.335 872 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.01 % Allowed : 16.28 % Favored : 81.71 % 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: -1.68 (0.32), residues: 721 helix: 1.22 (0.39), residues: 199 sheet: -2.18 (0.42), residues: 125 loop : -2.05 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.022 0.002 TYR A 859 PHE 0.029 0.002 PHE A 852 TRP 0.018 0.002 TRP A 605 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 5962) covalent geometry : angle 0.59727 / 0.30 ( 8112) hydrogen bonds : bond 0.03389 / 2.34 ( 212) hydrogen bonds : angle 5.25501 / 3.74 ( 621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8704 (m-80) cc_final: 0.8135 (m-80) REVERT: A 658 MET cc_start: 0.8561 (tpp) cc_final: 0.8314 (tmm) REVERT: A 680 ARG cc_start: 0.7399 (tmm160) cc_final: 0.7132 (tmm160) REVERT: A 792 MET cc_start: 0.7461 (mmm) cc_final: 0.7131 (mmm) outliers start: 12 outliers final: 12 residues processed: 79 average time/residue: 0.0670 time to fit residues: 7.4736 Evaluate side-chains 81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.091249 restraints weight = 10800.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091635 restraints weight = 7359.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092773 restraints weight = 6113.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093445 restraints weight = 5101.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093642 restraints weight = 4781.272| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5962 Z= 0.202 Angle : 0.603 13.414 8112 Z= 0.304 Chirality : 0.045 0.164 921 Planarity : 0.004 0.045 1018 Dihedral : 5.481 51.311 872 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.85 % Allowed : 17.11 % Favored : 81.04 % 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: -1.67 (0.32), residues: 721 helix: 1.22 (0.39), residues: 199 sheet: -2.20 (0.42), residues: 125 loop : -2.04 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.019 0.002 TYR A 244 PHE 0.023 0.002 PHE A 852 TRP 0.016 0.002 TRP A 605 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 5962) covalent geometry : angle 0.60267 / 0.30 ( 8112) hydrogen bonds : bond 0.03443 / 2.36 ( 212) hydrogen bonds : angle 5.29238 / 3.77 ( 621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8715 (m-80) cc_final: 0.8141 (m-80) REVERT: A 792 MET cc_start: 0.7404 (mmm) cc_final: 0.7086 (mmm) outliers start: 11 outliers final: 11 residues processed: 78 average time/residue: 0.0691 time to fit residues: 7.4735 Evaluate side-chains 80 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 13 optimal weight: 0.0270 chunk 26 optimal weight: 20.0000 chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 overall best weight: 3.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.121097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092482 restraints weight = 10712.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093475 restraints weight = 7126.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095063 restraints weight = 6027.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095458 restraints weight = 4445.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.096094 restraints weight = 4176.851| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5962 Z= 0.162 Angle : 0.600 13.416 8112 Z= 0.300 Chirality : 0.044 0.163 921 Planarity : 0.004 0.047 1018 Dihedral : 5.432 50.970 872 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.01 % Allowed : 16.95 % Favored : 81.04 % 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 (0.32), residues: 721 helix: 1.27 (0.39), residues: 199 sheet: -2.12 (0.43), residues: 125 loop : -2.01 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.019 0.001 TYR A 244 PHE 0.020 0.002 PHE A 852 TRP 0.012 0.001 TRP A 605 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 5962) covalent geometry : angle 0.60028 / 0.30 ( 8112) hydrogen bonds : bond 0.03308 / 2.27 ( 212) hydrogen bonds : angle 5.24037 / 3.73 ( 621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 251 MET cc_start: 0.7325 (ppp) cc_final: 0.6946 (ppp) REVERT: A 465 PHE cc_start: 0.8667 (m-80) cc_final: 0.8093 (m-80) REVERT: A 658 MET cc_start: 0.8539 (tpp) cc_final: 0.8335 (mmm) REVERT: A 680 ARG cc_start: 0.7437 (tmm160) cc_final: 0.7214 (tmm160) REVERT: A 792 MET cc_start: 0.7285 (mmm) cc_final: 0.6948 (mmm) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.0673 time to fit residues: 7.3439 Evaluate side-chains 80 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 959 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.119826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090994 restraints weight = 10753.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091313 restraints weight = 7343.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092348 restraints weight = 6122.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092969 restraints weight = 5178.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093120 restraints weight = 4840.217| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5962 Z= 0.228 Angle : 0.622 13.287 8112 Z= 0.313 Chirality : 0.045 0.162 921 Planarity : 0.004 0.045 1018 Dihedral : 5.517 51.056 872 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.35 % Allowed : 16.78 % Favored : 80.87 % 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: -1.64 (0.32), residues: 721 helix: 1.20 (0.39), residues: 199 sheet: -2.10 (0.42), residues: 132 loop : -2.01 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.019 0.002 TYR A 244 PHE 0.022 0.002 PHE A 852 TRP 0.015 0.002 TRP A 605 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 ( 5962) covalent geometry : angle 0.62168 / 0.31 ( 8112) hydrogen bonds : bond 0.03515 / 2.42 ( 212) hydrogen bonds : angle 5.31525 / 3.79 ( 621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 856.55 seconds wall clock time: 15 minutes 38.02 seconds (938.02 seconds total)