Starting phenix.real_space_refine on Fri Oct 23 03:09:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izs_61041/10_2026/9izs_61041.map" } resolution = 2.84 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 ------------------------------------------------------------------------------- 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= 0.011 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 101 5.49 5 Mg 5 5.21 5 S 36 5.16 5 C 4909 2.51 5 N 1389 2.21 5 O 1823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8263 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 6133 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 12, 'TRANS': 725} Chain: "B" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1127 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 19} Link IDs: {'rna2p': 9, 'rna3p': 43} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Classifications: {'DNA': 1} Chain: "D" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Unusual residues: {' GS': 3, ' SC': 1} Classifications: {'DNA': 29, 'undetermined': 4} Link IDs: {'rna3p': 27, None: 5} Not linked: pdbres=" GS D -2 " pdbres=" GS D -1 " Not linked: pdbres=" GS D -1 " pdbres="PST D 0 " Not linked: pdbres="PST D 0 " pdbres=" GS D 1 " Not linked: pdbres=" GS D 1 " pdbres=" SC D 2 " Not linked: pdbres=" SC D 2 " pdbres=" DC D 3 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: 1.62, per 1000 atoms: 0.20 Number of scatterers: 8263 At special positions: 0 Unit cell: (90.885, 98.355, 109.56, 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 36 16.00 P 101 15.00 Mg 5 11.99 O 1823 8.00 N 1389 7.00 C 4909 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 184.1 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 7 sheets defined 53.7% alpha, 10.2% beta 33 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.547A pdb=" N MET A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.837A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.562A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.879A pdb=" N GLU A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.208A pdb=" N ASP A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.541A pdb=" N THR A 359 " --> pdb=" O HIS A 355 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 397 through 419 Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.921A pdb=" N VAL A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 479 through 482 Processing helix chain 'A' and resid 483 through 518 removed outlier: 3.716A pdb=" N ASN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 547 Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.708A pdb=" N MET A 607 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.579A pdb=" N GLU A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.637A pdb=" N TYR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 690 " --> pdb=" O ASN A 686 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 720 through 731 removed outlier: 3.690A pdb=" N ILE A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE A 5 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.712A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 523 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL A 633 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 525 " --> pdb=" O VAL A 633 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 5.402A pdb=" N VAL A 377 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 574 through 578 removed outlier: 3.637A pdb=" N ASP A 586 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 659 through 660 removed outlier: 5.571A pdb=" N LEU A 648 " --> pdb=" O LYS A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 673 removed outlier: 3.602A pdb=" N LEU A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 3424 1.39 - 1.57: 4948 1.57 - 1.75: 193 1.75 - 1.93: 50 1.93 - 2.11: 3 Bond restraints: 8618 Sorted by residual: bond pdb=" C3' DA D 22 " pdb=" C2' DA D 22 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DC D 19 " pdb=" C2' DC D 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DA C 4 " pdb=" C2' DA C 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" O5' GS D -2 " pdb=" P GS D -2 " ideal model delta sigma weight residual 1.632 1.568 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O5' GS D -1 " pdb=" P GS D -1 " ideal model delta sigma weight residual 1.632 1.572 0.060 2.00e-02 2.50e+03 9.07e+00 ... (remaining 8613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11800 2.25 - 4.51: 237 4.51 - 6.76: 5 6.76 - 9.01: 3 9.01 - 11.27: 3 Bond angle restraints: 12048 Sorted by residual: angle pdb=" O5' A B -3 " pdb=" C5' A B -3 " pdb=" C4' A B -3 " ideal model delta sigma weight residual 109.40 113.11 -3.71 8.00e-01 1.56e+00 2.15e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT C -6 " pdb=" C4 DT C -6 " pdb=" O4 DT C -6 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT D 13 " pdb=" C4 DT D 13 " pdb=" O4 DT D 13 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 12043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.61: 4540 19.61 - 39.23: 424 39.23 - 58.84: 220 58.84 - 78.45: 65 78.45 - 98.06: 4 Dihedral angle restraints: 5253 sinusoidal: 3046 harmonic: 2207 Sorted by residual: dihedral pdb=" CA ARG A 420 " pdb=" C ARG A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" N LYS A 664 " pdb=" CA LYS A 664 " pdb=" CB LYS A 664 " pdb=" CG LYS A 664 " ideal model delta sinusoidal sigma weight residual -60.00 -117.97 57.97 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" O5' G B -13 " pdb=" C5' G B -13 " pdb=" C4' G B -13 " pdb=" C3' G B -13 " ideal model delta sinusoidal sigma weight residual 55.00 112.57 -57.57 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 5250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 850 0.038 - 0.076: 352 0.076 - 0.114: 98 0.114 - 0.152: 60 0.152 - 0.189: 2 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C3' PST D 0 " pdb=" C4' PST D 0 " pdb=" O3' PST D 0 " pdb=" C2' PST D 0 " both_signs ideal model delta sigma weight residual False -2.57 -2.76 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C3' SC D 2 " pdb=" C2' SC D 2 " pdb=" C4' SC D 2 " pdb=" O3' SC D 2 " both_signs ideal model delta sigma weight residual False -2.56 -2.74 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" C2' A B -3 " pdb=" C3' A B -3 " pdb=" O2' A B -3 " pdb=" C1' A B -3 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1359 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' PST D -3 " -0.184 2.00e-02 2.50e+03 8.50e-02 1.63e+02 pdb=" N1 PST D -3 " 0.065 2.00e-02 2.50e+03 pdb=" C2 PST D -3 " 0.038 2.00e-02 2.50e+03 pdb=" O2 PST D -3 " 0.072 2.00e-02 2.50e+03 pdb=" N3 PST D -3 " -0.028 2.00e-02 2.50e+03 pdb=" C4 PST D -3 " -0.028 2.00e-02 2.50e+03 pdb=" O4 PST D -3 " -0.079 2.00e-02 2.50e+03 pdb=" C5 PST D -3 " 0.039 2.00e-02 2.50e+03 pdb=" C6 PST D -3 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' PST D 0 " 0.098 2.00e-02 2.50e+03 5.25e-02 6.21e+01 pdb=" N1 PST D 0 " -0.014 2.00e-02 2.50e+03 pdb=" C2 PST D 0 " 0.005 2.00e-02 2.50e+03 pdb=" O2 PST D 0 " -0.078 2.00e-02 2.50e+03 pdb=" N3 PST D 0 " 0.040 2.00e-02 2.50e+03 pdb=" C4 PST D 0 " 0.011 2.00e-02 2.50e+03 pdb=" O4 PST D 0 " 0.040 2.00e-02 2.50e+03 pdb=" C5 PST D 0 " -0.042 2.00e-02 2.50e+03 pdb=" C6 PST D 0 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GS D -2 " 0.055 2.00e-02 2.50e+03 2.19e-02 1.43e+01 pdb=" C2 GS D -2 " 0.001 2.00e-02 2.50e+03 pdb=" C4 GS D -2 " -0.020 2.00e-02 2.50e+03 pdb=" C5 GS D -2 " -0.015 2.00e-02 2.50e+03 pdb=" C6 GS D -2 " 0.008 2.00e-02 2.50e+03 pdb=" C8 GS D -2 " -0.015 2.00e-02 2.50e+03 pdb=" N1 GS D -2 " 0.015 2.00e-02 2.50e+03 pdb=" N2 GS D -2 " -0.011 2.00e-02 2.50e+03 pdb=" N3 GS D -2 " -0.015 2.00e-02 2.50e+03 pdb=" N7 GS D -2 " -0.012 2.00e-02 2.50e+03 pdb=" N9 GS D -2 " -0.019 2.00e-02 2.50e+03 pdb=" O6 GS D -2 " 0.027 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 98 2.61 - 3.18: 6671 3.18 - 3.75: 13322 3.75 - 4.33: 19948 4.33 - 4.90: 29298 Nonbonded interactions: 69337 Sorted by model distance: nonbonded pdb=" OD2 ASP A 324 " pdb="MG MG A 803 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP A 324 " pdb="MG MG A 802 " model vdw 2.041 2.170 nonbonded pdb=" OP1 GS D -1 " pdb="MG MG A 802 " model vdw 2.053 2.170 nonbonded pdb=" OD1 ASN A 326 " pdb="MG MG A 803 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A 801 " model vdw 2.101 2.170 ... (remaining 69332 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.680 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.005 0.064 8624 Z= 0.370 Angle : 0.696 11.267 12048 Z= 0.507 Chirality : 0.049 0.189 1362 Planarity : 0.004 0.085 1170 Dihedral : 18.799 98.064 3827 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.87 % Allowed : 4.65 % Favored : 94.48 % 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: 0.07 (0.31), residues: 736 helix: 0.98 (0.27), residues: 357 sheet: -0.22 (0.61), residues: 75 loop : -0.96 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.023 0.002 TYR A 437 PHE 0.012 0.002 PHE A 603 TRP 0.014 0.002 TRP A 33 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.36 ( 8618) covalent geometry : angle 0.69641 / 0.51 (12048) hydrogen bonds : bond 0.18189 / 11.44 ( 380) hydrogen bonds : angle 5.65920 / 3.91 ( 1022) Misc. bond : bond 0.02947 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8083 (m-40) cc_final: 0.7834 (t0) REVERT: A 152 ASP cc_start: 0.8662 (m-30) cc_final: 0.8216 (m-30) REVERT: A 167 ASN cc_start: 0.7723 (m-40) cc_final: 0.7306 (m-40) REVERT: A 182 VAL cc_start: 0.6792 (p) cc_final: 0.6512 (m) REVERT: A 188 ASP cc_start: 0.7385 (t0) cc_final: 0.6979 (t0) REVERT: A 325 VAL cc_start: 0.8058 (t) cc_final: 0.7834 (t) REVERT: A 326 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7137 (m110) REVERT: A 498 GLN cc_start: 0.8251 (tt0) cc_final: 0.7926 (tt0) REVERT: A 557 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7578 (m110) REVERT: A 726 HIS cc_start: 0.6906 (t70) cc_final: 0.6522 (t-90) outliers start: 6 outliers final: 2 residues processed: 165 average time/residue: 0.6136 time to fit residues: 106.8846 Evaluate side-chains 113 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 557 ASN Chi-restraints excluded: chain A residue 670 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 HIS A 165 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 498 GLN A 506 ASN A 509 ASN A 517 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.187692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156680 restraints weight = 10301.712| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.57 r_work: 0.3822 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3687 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8624 Z= 0.193 Angle : 0.616 6.283 12048 Z= 0.345 Chirality : 0.042 0.206 1362 Planarity : 0.004 0.047 1170 Dihedral : 21.110 96.683 2229 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.33 % Allowed : 14.53 % Favored : 83.14 % 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: 0.23 (0.31), residues: 736 helix: 0.99 (0.26), residues: 371 sheet: 0.21 (0.65), residues: 73 loop : -0.89 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 133 TYR 0.023 0.002 TYR A 437 PHE 0.017 0.002 PHE A 478 TRP 0.017 0.002 TRP A 33 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 ( 8618) covalent geometry : angle 0.61620 / 0.34 (12048) hydrogen bonds : bond 0.06379 / 3.95 ( 380) hydrogen bonds : angle 4.45608 / 3.08 ( 1022) Misc. bond : bond 0.00206 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8292 (m-40) cc_final: 0.7985 (t0) REVERT: A 182 VAL cc_start: 0.6767 (p) cc_final: 0.6417 (m) REVERT: A 517 GLN cc_start: 0.7233 (mt0) cc_final: 0.6841 (mt0) REVERT: A 546 LEU cc_start: 0.7948 (mt) cc_final: 0.7679 (mt) REVERT: A 575 GLU cc_start: 0.8162 (tt0) cc_final: 0.7506 (pp20) REVERT: A 660 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6767 (tttm) outliers start: 16 outliers final: 8 residues processed: 133 average time/residue: 0.6154 time to fit residues: 86.6130 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 670 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [22, 3, 1, 76, 32, 8, 4, 34, 42, 2, 38] chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.187806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157072 restraints weight = 10198.683| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.56 r_work: 0.3823 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8624 Z= 0.182 Angle : 0.596 6.787 12048 Z= 0.331 Chirality : 0.041 0.191 1362 Planarity : 0.004 0.045 1170 Dihedral : 20.875 96.409 2224 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.62 % Allowed : 16.57 % Favored : 80.81 % 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: 0.15 (0.31), residues: 736 helix: 0.91 (0.26), residues: 378 sheet: -0.06 (0.65), residues: 75 loop : -0.88 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.024 0.002 TYR A 437 PHE 0.035 0.002 PHE A 478 TRP 0.017 0.002 TRP A 33 HIS 0.006 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 8618) covalent geometry : angle 0.59554 / 0.33 (12048) hydrogen bonds : bond 0.05759 / 3.53 ( 380) hydrogen bonds : angle 4.33427 / 3.02 ( 1022) Misc. bond : bond 0.00188 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8320 (m-40) cc_final: 0.7996 (t0) REVERT: A 182 VAL cc_start: 0.7012 (p) cc_final: 0.6658 (m) REVERT: A 326 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6920 (m-40) REVERT: A 517 GLN cc_start: 0.7290 (mt0) cc_final: 0.6908 (mt0) REVERT: A 575 GLU cc_start: 0.8214 (tt0) cc_final: 0.7639 (pp20) REVERT: A 660 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7100 (tttm) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.5667 time to fit residues: 74.6856 Evaluate side-chains 117 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [70, 67, 58, 52, 30, 11, 44, 78, 40, 31, 77] chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 30 optimal weight: 0.0010 chunk 11 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 overall best weight: 3.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.187906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.156798 restraints weight = 10324.442| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.59 r_work: 0.3826 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8624 Z= 0.175 Angle : 0.585 6.190 12048 Z= 0.325 Chirality : 0.041 0.190 1362 Planarity : 0.003 0.044 1170 Dihedral : 20.740 95.906 2224 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.76 % Allowed : 16.42 % Favored : 80.81 % 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: 0.17 (0.31), residues: 736 helix: 0.91 (0.26), residues: 378 sheet: -0.01 (0.65), residues: 71 loop : -0.86 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.024 0.002 TYR A 437 PHE 0.017 0.002 PHE A 200 TRP 0.017 0.002 TRP A 33 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8618) covalent geometry : angle 0.58505 / 0.32 (12048) hydrogen bonds : bond 0.05490 / 3.36 ( 380) hydrogen bonds : angle 4.28106 / 3.00 ( 1022) Misc. bond : bond 0.00149 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8308 (m-40) cc_final: 0.7987 (t0) REVERT: A 182 VAL cc_start: 0.7050 (p) cc_final: 0.6685 (m) REVERT: A 326 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.6893 (m-40) REVERT: A 517 GLN cc_start: 0.7158 (mt0) cc_final: 0.6808 (mt0) REVERT: A 547 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7500 (mmpt) REVERT: A 567 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: A 575 GLU cc_start: 0.8258 (tt0) cc_final: 0.7611 (pp20) REVERT: A 660 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6930 (tttm) outliers start: 19 outliers final: 11 residues processed: 124 average time/residue: 0.5656 time to fit residues: 74.6409 Evaluate side-chains 116 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [67, 22, 4, 71, 73, 43, 46, 1, 19, 11, 40] chunk 67 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.188376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157232 restraints weight = 10354.692| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.61 r_work: 0.3833 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8624 Z= 0.167 Angle : 0.578 7.801 12048 Z= 0.321 Chirality : 0.040 0.188 1362 Planarity : 0.003 0.042 1170 Dihedral : 20.649 95.441 2224 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.34 % Allowed : 17.73 % Favored : 78.92 % 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: 0.25 (0.31), residues: 736 helix: 0.97 (0.26), residues: 377 sheet: -0.02 (0.65), residues: 71 loop : -0.79 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.025 0.002 TYR A 437 PHE 0.013 0.001 PHE A 478 TRP 0.018 0.002 TRP A 33 HIS 0.006 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 8618) covalent geometry : angle 0.57837 / 0.32 (12048) hydrogen bonds : bond 0.05575 / 3.50 ( 380) hydrogen bonds : angle 4.26552 / 3.00 ( 1022) Misc. bond : bond 0.00129 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8334 (m-40) cc_final: 0.8004 (t0) REVERT: A 182 VAL cc_start: 0.7137 (p) cc_final: 0.6757 (m) REVERT: A 205 ASN cc_start: 0.7657 (m-40) cc_final: 0.7412 (p0) REVERT: A 308 TYR cc_start: 0.7221 (t80) cc_final: 0.6953 (t80) REVERT: A 326 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6910 (m-40) REVERT: A 478 PHE cc_start: 0.8635 (m-80) cc_final: 0.8337 (m-80) REVERT: A 567 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: A 607 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7512 (mmt) REVERT: A 660 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7079 (tttm) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.5408 time to fit residues: 71.5269 Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [80, 12, 33, 77, 16, 21, 47, 42, 71, 40, 64] chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A 509 ASN A 670 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.187583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156056 restraints weight = 10179.189| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.58 r_work: 0.3816 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8624 Z= 0.196 Angle : 0.608 7.072 12048 Z= 0.334 Chirality : 0.041 0.189 1362 Planarity : 0.003 0.045 1170 Dihedral : 20.649 95.234 2224 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.63 % Allowed : 17.88 % Favored : 78.49 % 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: 0.13 (0.31), residues: 736 helix: 0.84 (0.26), residues: 377 sheet: -0.02 (0.65), residues: 70 loop : -0.80 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.026 0.002 TYR A 437 PHE 0.014 0.002 PHE A 332 TRP 0.020 0.003 TRP A 33 HIS 0.006 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 8618) covalent geometry : angle 0.60782 / 0.33 (12048) hydrogen bonds : bond 0.05617 / 3.46 ( 380) hydrogen bonds : angle 4.30587 / 3.03 ( 1022) Misc. bond : bond 0.00128 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8332 (m-40) cc_final: 0.7996 (t0) REVERT: A 182 VAL cc_start: 0.7069 (p) cc_final: 0.6735 (m) REVERT: A 308 TYR cc_start: 0.7242 (t80) cc_final: 0.6953 (t80) REVERT: A 309 GLU cc_start: 0.7153 (pm20) cc_final: 0.6930 (pm20) REVERT: A 326 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.6865 (m-40) REVERT: A 418 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8353 (mt-10) REVERT: A 478 PHE cc_start: 0.8566 (m-80) cc_final: 0.8331 (m-80) REVERT: A 567 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: A 607 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7565 (mmt) REVERT: A 660 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6929 (tttm) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 0.5220 time to fit residues: 68.7124 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [80, 2, 78, 40, 15, 62, 33, 39, 16, 41, 24] chunk 80 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 ASN A 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.187520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.156157 restraints weight = 10380.672| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.58 r_work: 0.3817 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8624 Z= 0.181 Angle : 0.599 8.701 12048 Z= 0.328 Chirality : 0.041 0.185 1362 Planarity : 0.003 0.044 1170 Dihedral : 20.597 95.092 2224 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.05 % Allowed : 19.48 % Favored : 77.47 % 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: 0.13 (0.31), residues: 736 helix: 0.82 (0.26), residues: 377 sheet: -0.14 (0.64), residues: 71 loop : -0.74 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.027 0.002 TYR A 437 PHE 0.012 0.002 PHE A 332 TRP 0.020 0.002 TRP A 33 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 8618) covalent geometry : angle 0.59915 / 0.33 (12048) hydrogen bonds : bond 0.05475 / 3.36 ( 380) hydrogen bonds : angle 4.31811 / 3.05 ( 1022) Misc. bond : bond 0.00093 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8307 (m-40) cc_final: 0.8001 (t0) REVERT: A 182 VAL cc_start: 0.7135 (p) cc_final: 0.6757 (m) REVERT: A 205 ASN cc_start: 0.7855 (m-40) cc_final: 0.7601 (m110) REVERT: A 210 LYS cc_start: 0.8462 (mppt) cc_final: 0.8248 (mppt) REVERT: A 308 TYR cc_start: 0.7223 (t80) cc_final: 0.7010 (t80) REVERT: A 418 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8100 (mt-10) REVERT: A 478 PHE cc_start: 0.8651 (m-80) cc_final: 0.8392 (m-80) REVERT: A 567 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: A 607 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7561 (mmt) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 0.5415 time to fit residues: 67.5151 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [13, 11, 77, 14, 37, 68, 6, 66, 76, 36, 5] chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 ASN A 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.188438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156769 restraints weight = 10196.043| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.58 r_work: 0.3832 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8624 Z= 0.175 Angle : 0.604 9.174 12048 Z= 0.330 Chirality : 0.040 0.185 1362 Planarity : 0.003 0.043 1170 Dihedral : 20.550 95.083 2224 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.34 % Allowed : 19.62 % Favored : 77.03 % 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: 0.15 (0.31), residues: 736 helix: 0.83 (0.26), residues: 377 sheet: -0.17 (0.64), residues: 71 loop : -0.71 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.026 0.002 TYR A 437 PHE 0.012 0.002 PHE A 332 TRP 0.019 0.002 TRP A 33 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 8618) covalent geometry : angle 0.60395 / 0.33 (12048) hydrogen bonds : bond 0.05377 / 3.29 ( 380) hydrogen bonds : angle 4.30530 / 3.04 ( 1022) Misc. bond : bond 0.00080 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8323 (m-40) cc_final: 0.7999 (t0) REVERT: A 308 TYR cc_start: 0.7247 (t80) cc_final: 0.7006 (t80) REVERT: A 309 GLU cc_start: 0.7444 (pm20) cc_final: 0.7141 (pm20) REVERT: A 418 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8074 (mt-10) REVERT: A 478 PHE cc_start: 0.8646 (m-80) cc_final: 0.8383 (m-80) REVERT: A 567 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7248 (pt0) outliers start: 23 outliers final: 16 residues processed: 118 average time/residue: 0.4959 time to fit residues: 62.4721 Evaluate side-chains 111 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 356 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [2, 20, 60, 4, 79, 31, 24, 43, 34, 65, 70] chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 509 ASN A 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.189879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.158439 restraints weight = 10236.502| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.61 r_work: 0.3852 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8624 Z= 0.134 Angle : 0.565 9.483 12048 Z= 0.315 Chirality : 0.038 0.181 1362 Planarity : 0.003 0.039 1170 Dihedral : 20.396 94.762 2224 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.76 % Allowed : 20.35 % Favored : 76.89 % 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: 0.36 (0.31), residues: 736 helix: 1.00 (0.26), residues: 377 sheet: -0.07 (0.63), residues: 71 loop : -0.61 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 667 TYR 0.027 0.002 TYR A 159 PHE 0.011 0.001 PHE A 602 TRP 0.017 0.002 TRP A 33 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8618) covalent geometry : angle 0.56478 / 0.31 (12048) hydrogen bonds : bond 0.04870 / 2.99 ( 380) hydrogen bonds : angle 4.21183 / 2.98 ( 1022) Misc. bond : bond 0.00074 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8298 (m-40) cc_final: 0.7985 (t0) REVERT: A 308 TYR cc_start: 0.7191 (t80) cc_final: 0.6925 (t80) REVERT: A 309 GLU cc_start: 0.7405 (pm20) cc_final: 0.7131 (pm20) REVERT: A 478 PHE cc_start: 0.8689 (m-80) cc_final: 0.8419 (m-80) REVERT: A 567 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: A 575 GLU cc_start: 0.8209 (tt0) cc_final: 0.7759 (pp20) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.5471 time to fit residues: 68.2267 Evaluate side-chains 115 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [15, 63, 32, 55, 39, 19, 13, 62, 78, 14, 60] chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 ASN A 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156591 restraints weight = 10209.794| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.57 r_work: 0.3835 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8624 Z= 0.177 Angle : 0.613 9.826 12048 Z= 0.335 Chirality : 0.040 0.186 1362 Planarity : 0.003 0.042 1170 Dihedral : 20.370 95.049 2224 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.33 % Allowed : 21.37 % Favored : 76.31 % 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: 0.28 (0.31), residues: 736 helix: 0.91 (0.26), residues: 377 sheet: -0.15 (0.64), residues: 71 loop : -0.60 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.026 0.002 TYR A 437 PHE 0.012 0.002 PHE A 332 TRP 0.021 0.002 TRP A 33 HIS 0.005 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 ( 8618) covalent geometry : angle 0.61261 / 0.33 (12048) hydrogen bonds : bond 0.05267 / 3.22 ( 380) hydrogen bonds : angle 4.30977 / 3.05 ( 1022) Misc. bond : bond 0.00080 / 0.04 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8303 (m-40) cc_final: 0.7988 (t0) REVERT: A 308 TYR cc_start: 0.7211 (t80) cc_final: 0.6985 (t80) REVERT: A 309 GLU cc_start: 0.7412 (pm20) cc_final: 0.7165 (pm20) REVERT: A 418 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8144 (mt-10) REVERT: A 478 PHE cc_start: 0.8679 (m-80) cc_final: 0.8395 (m-80) REVERT: A 534 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7965 (tt0) REVERT: A 567 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7254 (pt0) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.5196 time to fit residues: 63.9091 Evaluate side-chains 109 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: [31, 25, 44, 26, 38, 51, 40, 77, 66, 41, 24] chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 509 ASN A 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.189847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.158802 restraints weight = 10259.986| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.59 r_work: 0.3856 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8624 Z= 0.142 Angle : 0.580 9.656 12048 Z= 0.321 Chirality : 0.038 0.184 1362 Planarity : 0.003 0.037 1170 Dihedral : 20.234 94.722 2224 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.18 % Allowed : 21.66 % Favored : 76.16 % 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: 0.40 (0.31), residues: 736 helix: 1.02 (0.26), residues: 378 sheet: -0.05 (0.64), residues: 71 loop : -0.58 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.025 0.002 TYR A 437 PHE 0.019 0.001 PHE A 478 TRP 0.019 0.002 TRP A 33 HIS 0.004 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 8618) covalent geometry : angle 0.58006 / 0.32 (12048) hydrogen bonds : bond 0.04877 / 3.00 ( 380) hydrogen bonds : angle 4.24067 / 3.00 ( 1022) Misc. bond : bond 0.00073 / 0.04 ( 6) =============================================================================== Job complete usr+sys time: 2981.55 seconds wall clock time: 51 minutes 35.39 seconds (3095.39 seconds total)