Starting phenix.real_space_refine on Tue Mar 3 14:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kx7_23061/03_2026/7kx7_23061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kx7_23061/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2026/7kx7_23061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2026/7kx7_23061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_2026/7kx7_23061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kx7_23061/03_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-5986/lib/python3.9/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: 1.63, per 1000 atoms: 0.28 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: 0.68 Conformation dependent library (CDL) restraints added in 157.4 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: 0.15 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: 0.92 Time building geometry restraints manager: 0.86 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: 3276 17.39 - 34.78: 281 34.78 - 52.16: 38 52.16 - 69.55: 14 69.55 - 86.94: 10 Dihedral angle restraints: 3619 sinusoidal: 1477 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 3616 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: 0.050 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 13.856 86.937 2231 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 covalent geometry : bond 0.00742 ( 5962) covalent geometry : angle 0.78647 ( 8112) hydrogen bonds : bond 0.21224 ( 212) hydrogen bonds : angle 9.63613 ( 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 : 0.246 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: 0.0913 time to fit residues: 10.2361 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 : 0.220 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.120398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091781 restraints weight = 10757.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092197 restraints weight = 7254.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093172 restraints weight = 5908.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.093613 restraints weight = 5123.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093920 restraints weight = 4750.456| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1304 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= 0.178 Angle : 0.612 7.835 8112 Z= 0.318 Chirality : 0.046 0.219 921 Planarity : 0.005 0.047 1018 Dihedral : 8.987 73.638 894 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.85 % Allowed : 8.56 % Favored : 89.60 % 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: -2.19 (0.32), residues: 721 helix: 0.70 (0.39), residues: 200 sheet: -2.25 (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 0.031 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 covalent geometry : bond 0.00407 ( 5962) covalent geometry : angle 0.61246 ( 8112) hydrogen bonds : bond 0.04474 ( 212) hydrogen bonds : angle 6.68639 ( 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 : 0.345 Fit side-chains REVERT: A 465 PHE cc_start: 0.8736 (m-80) cc_final: 0.8379 (m-80) REVERT: A 517 MET cc_start: 0.7710 (mpp) cc_final: 0.7489 (mpp) REVERT: A 680 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6905 (tmm160) REVERT: A 902 ASP cc_start: 0.7616 (p0) cc_final: 0.7287 (p0) outliers start: 11 outliers final: 4 residues processed: 84 average time/residue: 0.0706 time to fit residues: 8.2571 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 : 0.219 ------------------------------------------------------------------------------- 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: 9.9990 chunk 2 optimal weight: 50.0000 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3572 r_free = 0.3572 target = 0.119379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090496 restraints weight = 10746.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090829 restraints weight = 7404.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091844 restraints weight = 6130.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092181 restraints weight = 5191.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.092553 restraints weight = 4869.796| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1512 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= 0.222 Angle : 0.597 9.917 8112 Z= 0.309 Chirality : 0.046 0.220 921 Planarity : 0.004 0.048 1018 Dihedral : 8.843 73.792 894 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.35 % Allowed : 12.08 % Favored : 85.57 % 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: -2.05 (0.32), residues: 721 helix: 0.79 (0.39), residues: 205 sheet: -2.19 (0.39), residues: 141 loop : -2.33 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 607 TYR 0.020 0.002 TYR A 859 PHE 0.028 0.002 PHE A 528 TRP 0.009 0.002 TRP A 623 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 5962) covalent geometry : angle 0.59681 ( 8112) hydrogen bonds : bond 0.04226 ( 212) hydrogen bonds : angle 6.19594 ( 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 81 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.192 Fit side-chains REVERT: A 465 PHE cc_start: 0.8732 (m-80) cc_final: 0.8340 (m-80) REVERT: A 573 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8082 (mp) REVERT: A 605 TRP cc_start: 0.8878 (p90) cc_final: 0.8600 (p90) outliers start: 14 outliers final: 7 residues processed: 74 average time/residue: 0.0649 time to fit residues: 6.7904 Evaluate side-chains 73 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3574 r_free = 0.3574 target = 0.119458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090877 restraints weight = 10842.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090432 restraints weight = 7797.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.092607 restraints weight = 6535.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093096 restraints weight = 4698.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093365 restraints weight = 4746.525| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1686 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= 0.213 Angle : 0.589 7.936 8112 Z= 0.306 Chirality : 0.046 0.207 921 Planarity : 0.004 0.048 1018 Dihedral : 8.809 73.763 894 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.68 % Allowed : 13.42 % 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: 0.83 (0.39), residues: 205 sheet: -2.19 (0.39), residues: 142 loop : -2.30 (0.33), residues: 374 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 0.022 0.002 PHE A 406 TRP 0.008 0.001 TRP A 623 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 5962) covalent geometry : angle 0.58871 ( 8112) hydrogen bonds : bond 0.03893 ( 212) hydrogen bonds : angle 5.96011 ( 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: 10 poor density : 67 time to evaluate : 0.224 Fit side-chains REVERT: A 465 PHE cc_start: 0.8680 (m-80) cc_final: 0.8282 (m-80) REVERT: A 605 TRP cc_start: 0.8904 (p90) cc_final: 0.8588 (p90) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.0647 time to fit residues: 6.5176 Evaluate side-chains 69 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093535 restraints weight = 10800.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094042 restraints weight = 7130.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095275 restraints weight = 5866.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095781 restraints weight = 4864.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.095909 restraints weight = 4581.774| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1973 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= 0.124 Angle : 0.546 9.386 8112 Z= 0.279 Chirality : 0.044 0.176 921 Planarity : 0.004 0.049 1018 Dihedral : 8.620 73.539 894 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.68 % Allowed : 14.09 % Favored : 84.23 % 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: 1.19 (0.40), residues: 199 sheet: -2.28 (0.39), residues: 131 loop : -1.99 (0.32), residues: 391 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 0.019 0.002 PHE A 406 TRP 0.008 0.001 TRP A 623 HIS 0.004 0.000 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5962) covalent geometry : angle 0.54577 ( 8112) hydrogen bonds : bond 0.03373 ( 212) hydrogen bonds : angle 5.51822 ( 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 87 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8674 (m-80) cc_final: 0.8211 (m-80) outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.0728 time to fit residues: 8.2566 Evaluate side-chains 77 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 683 MET 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: 9.9990 chunk 24 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3572 r_free = 0.3572 target = 0.118922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090022 restraints weight = 10816.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.090382 restraints weight = 7407.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.091668 restraints weight = 6212.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.092029 restraints weight = 5087.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092321 restraints weight = 4813.122| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 5962 Z= 0.268 Angle : 0.652 15.343 8112 Z= 0.328 Chirality : 0.046 0.198 921 Planarity : 0.005 0.045 1018 Dihedral : 8.700 73.894 894 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.52 % Allowed : 14.60 % Favored : 82.89 % 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: -1.80 (0.32), residues: 721 helix: 1.10 (0.39), residues: 199 sheet: -2.17 (0.40), residues: 146 loop : -2.11 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.019 0.002 TYR A 859 PHE 0.028 0.002 PHE A 406 TRP 0.037 0.003 TRP A 605 HIS 0.007 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00628 ( 5962) covalent geometry : angle 0.65221 ( 8112) hydrogen bonds : bond 0.03729 ( 212) hydrogen bonds : angle 5.58147 ( 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 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8719 (m-80) cc_final: 0.8233 (m-80) REVERT: A 658 MET cc_start: 0.8608 (tpp) cc_final: 0.8332 (tmm) outliers start: 15 outliers final: 12 residues processed: 81 average time/residue: 0.0744 time to fit residues: 8.3044 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 : 0.236 ------------------------------------------------------------------------------- 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 478 THR 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 761 VAL 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: 6.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3586 r_free = 0.3586 target = 0.120020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.091482 restraints weight = 10694.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091997 restraints weight = 7180.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093829 restraints weight = 6040.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094255 restraints weight = 4583.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094596 restraints weight = 4350.896| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5962 Z= 0.193 Angle : 0.609 13.787 8112 Z= 0.307 Chirality : 0.045 0.169 921 Planarity : 0.004 0.047 1018 Dihedral : 8.666 73.731 894 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.35 % Allowed : 15.10 % 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: -1.80 (0.32), residues: 721 helix: 1.12 (0.39), residues: 199 sheet: -2.16 (0.40), residues: 146 loop : -2.13 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 354 TYR 0.021 0.002 TYR A 859 PHE 0.031 0.002 PHE A 852 TRP 0.020 0.002 TRP A 605 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 5962) covalent geometry : angle 0.60871 ( 8112) hydrogen bonds : bond 0.03523 ( 212) hydrogen bonds : angle 5.48151 ( 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 86 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8718 (m-80) cc_final: 0.8153 (m-80) REVERT: A 658 MET cc_start: 0.8544 (tpp) cc_final: 0.8316 (tmm) REVERT: A 680 ARG cc_start: 0.7357 (tmm160) cc_final: 0.7112 (tmm160) outliers start: 14 outliers final: 13 residues processed: 82 average time/residue: 0.0707 time to fit residues: 7.9673 Evaluate side-chains 82 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 444 ASP 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 761 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: 5.9990 chunk 41 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 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 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 = 0.3605 r_free = 0.3605 target = 0.121196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092453 restraints weight = 10687.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092950 restraints weight = 7286.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094410 restraints weight = 6069.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094548 restraints weight = 4849.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095347 restraints weight = 4632.874| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2245 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= 0.171 Angle : 0.597 13.311 8112 Z= 0.301 Chirality : 0.045 0.166 921 Planarity : 0.004 0.048 1018 Dihedral : 8.612 73.680 894 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.52 % Allowed : 15.44 % 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: -1.75 (0.32), residues: 721 helix: 1.18 (0.39), residues: 199 sheet: -2.24 (0.42), residues: 125 loop : -2.11 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.021 0.002 TYR A 859 PHE 0.026 0.002 PHE A 852 TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5962) covalent geometry : angle 0.59687 ( 8112) hydrogen bonds : bond 0.03390 ( 212) hydrogen bonds : angle 5.37452 ( 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 88 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8684 (m-80) cc_final: 0.8131 (m-80) REVERT: A 658 MET cc_start: 0.8535 (tpp) cc_final: 0.8294 (tmm) REVERT: A 680 ARG cc_start: 0.7393 (tmm160) cc_final: 0.7123 (tmm160) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.0698 time to fit residues: 8.0016 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 444 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 614 VAL 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 761 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 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 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.120833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092134 restraints weight = 10777.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093021 restraints weight = 7116.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094959 restraints weight = 5497.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094879 restraints weight = 4543.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095341 restraints weight = 4279.839| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5962 Z= 0.155 Angle : 0.597 13.478 8112 Z= 0.298 Chirality : 0.044 0.163 921 Planarity : 0.004 0.048 1018 Dihedral : 8.572 73.638 894 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.68 % Allowed : 15.94 % Favored : 81.38 % 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: 1.25 (0.40), residues: 199 sheet: -2.19 (0.42), residues: 125 loop : -2.06 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 354 TYR 0.020 0.002 TYR A 244 PHE 0.026 0.002 PHE A 852 TRP 0.013 0.001 TRP A 605 HIS 0.005 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5962) covalent geometry : angle 0.59712 ( 8112) hydrogen bonds : bond 0.03315 ( 212) hydrogen bonds : angle 5.30701 ( 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 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8687 (m-80) cc_final: 0.8103 (m-80) REVERT: A 658 MET cc_start: 0.8560 (tpp) cc_final: 0.8329 (tmm) REVERT: A 792 MET cc_start: 0.7358 (mmm) cc_final: 0.6969 (mmm) REVERT: A 959 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8497 (m110) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.0689 time to fit residues: 7.7865 Evaluate side-chains 83 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 614 VAL 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 761 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 42 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.121151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.092537 restraints weight = 10734.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093451 restraints weight = 7109.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095108 restraints weight = 6000.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095462 restraints weight = 4453.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095667 restraints weight = 4431.962| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2378 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= 0.160 Angle : 0.594 13.550 8112 Z= 0.297 Chirality : 0.044 0.163 921 Planarity : 0.004 0.048 1018 Dihedral : 8.542 73.653 894 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.52 % Allowed : 15.94 % Favored : 81.54 % 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: 1.28 (0.40), residues: 199 sheet: -1.91 (0.43), residues: 134 loop : -2.14 (0.32), residues: 388 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 0.024 0.002 PHE A 406 TRP 0.012 0.001 TRP A 605 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 5962) covalent geometry : angle 0.59413 ( 8112) hydrogen bonds : bond 0.03318 ( 212) hydrogen bonds : angle 5.27245 ( 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 85 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 465 PHE cc_start: 0.8672 (m-80) cc_final: 0.8098 (m-80) REVERT: A 680 ARG cc_start: 0.7455 (tmm160) cc_final: 0.7225 (tmm160) REVERT: A 792 MET cc_start: 0.7319 (mmm) cc_final: 0.6933 (mmm) outliers start: 15 outliers final: 14 residues processed: 81 average time/residue: 0.0695 time to fit residues: 7.8340 Evaluate side-chains 84 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 614 VAL 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 761 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: 0.0870 chunk 43 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 overall best weight: 4.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3607 r_free = 0.3607 target = 0.121540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.093062 restraints weight = 10709.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093910 restraints weight = 7024.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.095585 restraints weight = 5913.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095990 restraints weight = 4432.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096278 restraints weight = 4443.688| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5962 Z= 0.169 Angle : 0.588 13.203 8112 Z= 0.296 Chirality : 0.044 0.163 921 Planarity : 0.004 0.050 1018 Dihedral : 8.527 73.676 894 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.52 % Allowed : 15.94 % Favored : 81.54 % 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: -1.52 (0.33), residues: 721 helix: 1.43 (0.40), residues: 193 sheet: -1.79 (0.42), residues: 139 loop : -2.05 (0.32), residues: 389 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 0.022 0.002 PHE A 406 TRP 0.012 0.001 TRP A 605 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5962) covalent geometry : angle 0.58753 ( 8112) hydrogen bonds : bond 0.03319 ( 212) hydrogen bonds : angle 5.25114 ( 621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 885.28 seconds wall clock time: 16 minutes 3.06 seconds (963.06 seconds total)