Starting phenix.real_space_refine on Tue Aug 4 17:25:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw6_48678/08_2026/9mw6_48678.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 52 5.49 5 S 23 5.16 5 C 3259 2.51 5 N 958 2.21 5 O 1181 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5473 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4334 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 25, 'TRANS': 509} Chain breaks: 1 Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Time building chain proxies: 1.36, per 1000 atoms: 0.25 Number of scatterers: 5473 At special positions: 0 Unit cell: (74.12, 91.56, 106.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 52 15.00 O 1181 8.00 N 958 7.00 C 3259 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: 0.48 Conformation dependent library (CDL) restraints added in 161.6 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 48.0% alpha, 11.0% beta 27 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 4.159A pdb=" N LEU A 18 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.711A pdb=" N ALA A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 52 removed outlier: 3.889A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.811A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.586A pdb=" N MET A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.835A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.650A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 187 through 200 removed outlier: 4.293A pdb=" N LYS A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.705A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 344 through 362 removed outlier: 3.701A pdb=" N LYS A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.649A pdb=" N TYR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.687A pdb=" N ILE A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.502A pdb=" N GLY A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.766A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 4.065A pdb=" N ASP A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 564 removed outlier: 3.756A pdb=" N LEU A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 632 removed outlier: 3.895A pdb=" N LYS A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.578A pdb=" N VAL A 116 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ARG A 62 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 139 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 64 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 141 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU A 66 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASN A 137 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N LEU A 172 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU A 139 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU A 174 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE A 141 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 228 removed outlier: 3.580A pdb=" N TYR A 486 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 228 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 489 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.602A pdb=" N GLY A 370 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA A 444 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 372 " --> pdb=" O ALA A 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 582 removed outlier: 3.520A pdb=" N ILE A 579 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 591 " --> pdb=" O ILE A 579 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1548 1.34 - 1.46: 1346 1.46 - 1.58: 2654 1.58 - 1.70: 104 1.70 - 1.82: 35 Bond restraints: 5687 Sorted by residual: bond pdb=" N7 G B 27 " pdb=" C5 G B 27 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.92e+00 bond pdb=" N9 G B 27 " pdb=" C8 G B 27 " ideal model delta sigma weight residual 1.374 1.363 0.011 7.00e-03 2.04e+04 2.54e+00 bond pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" CA LYS A 436 " pdb=" CB LYS A 436 " ideal model delta sigma weight residual 1.529 1.551 -0.023 1.64e-02 3.72e+03 1.92e+00 bond pdb=" C2 U B 19 " pdb=" N3 U B 19 " ideal model delta sigma weight residual 1.373 1.365 0.008 7.00e-03 2.04e+04 1.34e+00 ... (remaining 5682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 7783 2.37 - 4.73: 124 4.73 - 7.10: 2 7.10 - 9.46: 5 9.46 - 11.83: 4 Bond angle restraints: 7918 Sorted by residual: angle pdb=" CA LYS A 436 " pdb=" CB LYS A 436 " pdb=" CG LYS A 436 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 angle pdb=" CB LYS A 436 " pdb=" CG LYS A 436 " pdb=" CD LYS A 436 " ideal model delta sigma weight residual 111.30 121.05 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " pdb=" CD LYS A 355 " ideal model delta sigma weight residual 111.30 120.93 -9.63 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA LYS A 355 " pdb=" CB LYS A 355 " pdb=" CG LYS A 355 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.55e+01 ... (remaining 7913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3056 17.89 - 35.78: 346 35.78 - 53.67: 100 53.67 - 71.56: 50 71.56 - 89.45: 15 Dihedral angle restraints: 3567 sinusoidal: 1987 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ALA A 444 " pdb=" C ALA A 444 " pdb=" N THR A 445 " pdb=" CA THR A 445 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU A 507 " pdb=" CG GLU A 507 " pdb=" CD GLU A 507 " pdb=" OE1 GLU A 507 " ideal model delta sinusoidal sigma weight residual 0.00 89.45 -89.45 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA PHE A 405 " pdb=" C PHE A 405 " pdb=" N VAL A 406 " pdb=" CA VAL A 406 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 3564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 697 0.047 - 0.094: 139 0.094 - 0.141: 85 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 123 " pdb=" CB LEU A 123 " pdb=" CD1 LEU A 123 " pdb=" CD2 LEU A 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2' U B 25 " pdb=" C3' U B 25 " pdb=" O2' U B 25 " pdb=" C1' U B 25 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C2' G B 27 " pdb=" C3' G B 27 " pdb=" O2' G B 27 " pdb=" C1' G B 27 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 923 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 151 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO A 152 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B 26 " 0.025 2.00e-02 2.50e+03 1.29e-02 3.76e+00 pdb=" N1 C B 26 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C B 26 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C B 26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B 26 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C B 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 26 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 436 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS A 436 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS A 436 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 437 " -0.010 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 5385 3.22 - 3.78: 9200 3.78 - 4.34: 11645 4.34 - 4.90: 17176 Nonbonded interactions: 43531 Sorted by model distance: nonbonded pdb=" O PRO A 597 " pdb=" OG SER A 600 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR A 69 " pdb=" OP1 C B 26 " model vdw 2.165 3.040 nonbonded pdb=" O LYS A 24 " pdb=" NH2 ARG A 170 " model vdw 2.256 3.120 nonbonded pdb=" OE1 GLU A 421 " pdb=" ND2 ASN A 423 " model vdw 2.275 3.120 nonbonded pdb=" OH TYR A 538 " pdb=" ND1 HIS A 630 " model vdw 2.275 3.120 ... (remaining 43526 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: 2.120 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.940 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.004 0.045 5687 Z= 0.212 Angle : 0.705 11.827 7918 Z= 0.451 Chirality : 0.050 0.235 926 Planarity : 0.004 0.049 820 Dihedral : 17.581 89.445 2537 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.43 % Allowed : 22.31 % Favored : 75.25 % 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 (0.38), residues: 531 helix: 1.18 (0.39), residues: 197 sheet: -0.50 (0.62), residues: 80 loop : -0.96 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.008 0.001 TYR A 384 PHE 0.012 0.002 PHE A 530 TRP 0.006 0.001 TRP A 100 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.21 ( 5687) covalent geometry : angle 0.70542 / 0.45 ( 7918) hydrogen bonds : bond 0.15234 / 10.66 ( 216) hydrogen bonds : angle 5.73045 / 4.13 ( 553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9036 (tp) cc_final: 0.8703 (tp) REVERT: A 43 MET cc_start: 0.9187 (mmm) cc_final: 0.8954 (mmm) REVERT: A 117 MET cc_start: 0.8630 (ptp) cc_final: 0.8038 (ptt) REVERT: A 143 GLU cc_start: 0.7754 (mp0) cc_final: 0.7265 (mp0) REVERT: A 355 LYS cc_start: 0.9605 (tppt) cc_final: 0.9221 (mttt) REVERT: A 448 VAL cc_start: 0.7649 (m) cc_final: 0.7287 (p) REVERT: A 462 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6607 (mmp80) REVERT: A 632 MET cc_start: 0.8723 (ppp) cc_final: 0.8449 (ppp) outliers start: 12 outliers final: 9 residues processed: 53 average time/residue: 0.0557 time to fit residues: 4.0664 Evaluate side-chains 54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 607 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.108437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.079651 restraints weight = 20389.290| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 5.41 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5687 Z= 0.139 Angle : 0.552 7.718 7918 Z= 0.294 Chirality : 0.038 0.152 926 Planarity : 0.004 0.048 820 Dihedral : 15.896 75.998 1415 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.65 % Allowed : 21.50 % Favored : 74.85 % 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 (0.38), residues: 531 helix: 1.07 (0.38), residues: 204 sheet: -0.32 (0.62), residues: 85 loop : -1.03 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.010 0.001 TYR A 560 PHE 0.012 0.001 PHE A 530 TRP 0.004 0.001 TRP A 100 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 5687) covalent geometry : angle 0.55222 / 0.29 ( 7918) hydrogen bonds : bond 0.04797 / 3.28 ( 216) hydrogen bonds : angle 4.61789 / 3.32 ( 553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8173 (mmt) cc_final: 0.7877 (mmm) REVERT: A 31 LEU cc_start: 0.9022 (tp) cc_final: 0.8690 (tp) REVERT: A 43 MET cc_start: 0.9182 (mmm) cc_final: 0.8939 (mmm) REVERT: A 117 MET cc_start: 0.8581 (ptp) cc_final: 0.8004 (ptt) REVERT: A 143 GLU cc_start: 0.7761 (mp0) cc_final: 0.7227 (mp0) REVERT: A 224 ILE cc_start: 0.7095 (mp) cc_final: 0.6849 (mp) REVERT: A 632 MET cc_start: 0.8715 (ppp) cc_final: 0.8421 (ppp) outliers start: 18 outliers final: 12 residues processed: 59 average time/residue: 0.0459 time to fit residues: 4.1649 Evaluate side-chains 54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.107711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079073 restraints weight = 20319.648| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 5.40 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5687 Z= 0.115 Angle : 0.518 6.329 7918 Z= 0.274 Chirality : 0.037 0.140 926 Planarity : 0.004 0.046 820 Dihedral : 15.626 75.812 1399 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.65 % Allowed : 21.91 % Favored : 74.44 % 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: 0.05 (0.38), residues: 531 helix: 1.23 (0.38), residues: 203 sheet: -0.37 (0.66), residues: 74 loop : -0.80 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.016 0.001 TYR A 217 PHE 0.009 0.001 PHE A 530 TRP 0.003 0.001 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 5687) covalent geometry : angle 0.51817 / 0.27 ( 7918) hydrogen bonds : bond 0.03919 / 2.63 ( 216) hydrogen bonds : angle 4.27001 / 3.09 ( 553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8173 (mmt) cc_final: 0.7894 (mmm) REVERT: A 31 LEU cc_start: 0.9068 (tp) cc_final: 0.8698 (tp) REVERT: A 43 MET cc_start: 0.9209 (mmm) cc_final: 0.8964 (mmm) REVERT: A 117 MET cc_start: 0.8499 (ptp) cc_final: 0.7939 (ptt) REVERT: A 125 ILE cc_start: 0.8230 (mm) cc_final: 0.8011 (tt) REVERT: A 143 GLU cc_start: 0.7779 (mp0) cc_final: 0.7265 (mp0) REVERT: A 224 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6928 (mp) REVERT: A 355 LYS cc_start: 0.9642 (tppt) cc_final: 0.9309 (mttt) REVERT: A 384 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 550 MET cc_start: 0.9154 (tmm) cc_final: 0.8799 (tpp) REVERT: A 632 MET cc_start: 0.8690 (ppp) cc_final: 0.8374 (ppp) outliers start: 18 outliers final: 9 residues processed: 63 average time/residue: 0.0543 time to fit residues: 5.0014 Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.108284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.079784 restraints weight = 20049.845| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 5.28 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5687 Z= 0.104 Angle : 0.503 7.473 7918 Z= 0.264 Chirality : 0.037 0.141 926 Planarity : 0.004 0.046 820 Dihedral : 15.589 75.567 1395 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.04 % Allowed : 24.34 % Favored : 72.62 % 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: 0.06 (0.38), residues: 531 helix: 1.09 (0.38), residues: 209 sheet: -0.49 (0.69), residues: 67 loop : -0.63 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.007 0.001 TYR A 357 PHE 0.009 0.001 PHE A 358 TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 5687) covalent geometry : angle 0.50349 / 0.26 ( 7918) hydrogen bonds : bond 0.03591 / 2.41 ( 216) hydrogen bonds : angle 4.12234 / 2.97 ( 553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8188 (mmt) cc_final: 0.7926 (mmm) REVERT: A 31 LEU cc_start: 0.9085 (tp) cc_final: 0.8716 (tp) REVERT: A 43 MET cc_start: 0.9171 (mmm) cc_final: 0.8902 (mmm) REVERT: A 117 MET cc_start: 0.8461 (ptp) cc_final: 0.7904 (ptt) REVERT: A 125 ILE cc_start: 0.8186 (mm) cc_final: 0.7965 (tt) REVERT: A 143 GLU cc_start: 0.7776 (mp0) cc_final: 0.7267 (mp0) REVERT: A 224 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 355 LYS cc_start: 0.9635 (tppt) cc_final: 0.9295 (mttt) REVERT: A 384 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8104 (t80) REVERT: A 501 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8969 (m-30) REVERT: A 632 MET cc_start: 0.8713 (ppp) cc_final: 0.8388 (ppp) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.0537 time to fit residues: 4.6830 Evaluate side-chains 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.107658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.078994 restraints weight = 20971.669| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.51 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5687 Z= 0.124 Angle : 0.503 6.886 7918 Z= 0.264 Chirality : 0.036 0.138 926 Planarity : 0.004 0.048 820 Dihedral : 15.585 75.613 1395 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.84 % Allowed : 24.34 % Favored : 72.82 % 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: 0.04 (0.38), residues: 531 helix: 1.11 (0.38), residues: 210 sheet: -0.48 (0.69), residues: 67 loop : -0.71 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.006 0.001 TYR A 357 PHE 0.010 0.001 PHE A 530 TRP 0.003 0.001 TRP A 100 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5687) covalent geometry : angle 0.50271 / 0.26 ( 7918) hydrogen bonds : bond 0.03827 / 2.62 ( 216) hydrogen bonds : angle 4.08167 / 2.95 ( 553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9058 (tp) cc_final: 0.8726 (tp) REVERT: A 43 MET cc_start: 0.9186 (mmm) cc_final: 0.8923 (mmm) REVERT: A 117 MET cc_start: 0.8459 (ptp) cc_final: 0.7900 (ptt) REVERT: A 143 GLU cc_start: 0.7811 (mp0) cc_final: 0.7309 (mp0) REVERT: A 224 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6987 (mp) REVERT: A 355 LYS cc_start: 0.9642 (tppt) cc_final: 0.9306 (mttt) REVERT: A 384 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7949 (t80) REVERT: A 632 MET cc_start: 0.8721 (ppp) cc_final: 0.8388 (ppp) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.0500 time to fit residues: 4.2504 Evaluate side-chains 54 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.108175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.079350 restraints weight = 20516.265| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 5.47 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5687 Z= 0.109 Angle : 0.505 8.087 7918 Z= 0.261 Chirality : 0.036 0.136 926 Planarity : 0.004 0.047 820 Dihedral : 15.586 75.603 1395 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.46 % Allowed : 23.12 % Favored : 72.41 % 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: 0.02 (0.38), residues: 531 helix: 1.09 (0.38), residues: 210 sheet: -0.30 (0.76), residues: 57 loop : -0.77 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.015 0.001 TYR A 217 PHE 0.009 0.001 PHE A 530 TRP 0.002 0.001 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5687) covalent geometry : angle 0.50525 / 0.26 ( 7918) hydrogen bonds : bond 0.03573 / 2.42 ( 216) hydrogen bonds : angle 4.01410 / 2.89 ( 553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7116 (p0) REVERT: A 31 LEU cc_start: 0.9064 (tp) cc_final: 0.8694 (tp) REVERT: A 43 MET cc_start: 0.9167 (mmm) cc_final: 0.8905 (mmm) REVERT: A 117 MET cc_start: 0.8455 (ptp) cc_final: 0.7894 (ptt) REVERT: A 143 GLU cc_start: 0.7868 (mp0) cc_final: 0.7383 (mp0) REVERT: A 224 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6971 (mp) REVERT: A 355 LYS cc_start: 0.9638 (tppt) cc_final: 0.9308 (mttt) REVERT: A 384 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 632 MET cc_start: 0.8708 (ppp) cc_final: 0.8373 (ppp) outliers start: 22 outliers final: 15 residues processed: 63 average time/residue: 0.0574 time to fit residues: 5.2496 Evaluate side-chains 61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 5 optimal weight: 6.9990 chunk 43 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.108878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.080432 restraints weight = 20453.492| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 5.46 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5687 Z= 0.096 Angle : 0.498 7.291 7918 Z= 0.256 Chirality : 0.036 0.148 926 Planarity : 0.004 0.047 820 Dihedral : 15.597 75.500 1395 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.25 % Allowed : 24.34 % Favored : 72.41 % 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: 0.05 (0.39), residues: 531 helix: 1.14 (0.38), residues: 210 sheet: -0.28 (0.76), residues: 57 loop : -0.78 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.006 0.001 TYR A 357 PHE 0.008 0.001 PHE A 358 TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 5687) covalent geometry : angle 0.49826 / 0.26 ( 7918) hydrogen bonds : bond 0.03225 / 2.16 ( 216) hydrogen bonds : angle 3.90399 / 2.80 ( 553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7189 (p0) REVERT: A 31 LEU cc_start: 0.9061 (tp) cc_final: 0.8697 (tp) REVERT: A 43 MET cc_start: 0.9151 (mmm) cc_final: 0.8878 (mmm) REVERT: A 53 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9085 (tpm170) REVERT: A 117 MET cc_start: 0.8372 (ptp) cc_final: 0.7815 (ptt) REVERT: A 143 GLU cc_start: 0.7804 (mp0) cc_final: 0.7316 (mp0) REVERT: A 224 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.7001 (mp) REVERT: A 355 LYS cc_start: 0.9633 (tppt) cc_final: 0.9297 (mttt) REVERT: A 384 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 632 MET cc_start: 0.8722 (ppp) cc_final: 0.8382 (ppp) outliers start: 16 outliers final: 11 residues processed: 58 average time/residue: 0.0578 time to fit residues: 4.8204 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 0.0010 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.108042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079496 restraints weight = 20258.355| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 5.41 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5687 Z= 0.120 Angle : 0.527 10.662 7918 Z= 0.267 Chirality : 0.037 0.138 926 Planarity : 0.004 0.048 820 Dihedral : 15.598 75.507 1395 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.85 % Allowed : 23.94 % Favored : 72.21 % 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: 0.06 (0.39), residues: 531 helix: 1.13 (0.38), residues: 210 sheet: -0.45 (0.69), residues: 67 loop : -0.71 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.016 0.001 TYR A 217 PHE 0.013 0.001 PHE A 56 TRP 0.003 0.001 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 5687) covalent geometry : angle 0.52674 / 0.27 ( 7918) hydrogen bonds : bond 0.03531 / 2.40 ( 216) hydrogen bonds : angle 3.96011 / 2.86 ( 553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7144 (p0) REVERT: A 31 LEU cc_start: 0.9046 (tp) cc_final: 0.8676 (tp) REVERT: A 43 MET cc_start: 0.9162 (mmm) cc_final: 0.8897 (mmm) REVERT: A 53 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9071 (tpm170) REVERT: A 117 MET cc_start: 0.8399 (ptp) cc_final: 0.7839 (ptt) REVERT: A 143 GLU cc_start: 0.7825 (mp0) cc_final: 0.7292 (mp0) REVERT: A 224 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 355 LYS cc_start: 0.9635 (tppt) cc_final: 0.9306 (mttt) REVERT: A 384 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.8056 (t80) REVERT: A 632 MET cc_start: 0.8737 (ppp) cc_final: 0.8397 (ppp) outliers start: 19 outliers final: 14 residues processed: 58 average time/residue: 0.0681 time to fit residues: 5.4598 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 21 optimal weight: 0.0050 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.109140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.080869 restraints weight = 20306.936| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 5.46 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5687 Z= 0.099 Angle : 0.518 8.578 7918 Z= 0.262 Chirality : 0.037 0.259 926 Planarity : 0.004 0.048 820 Dihedral : 15.599 75.502 1395 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.85 % Allowed : 24.14 % Favored : 72.01 % 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: 0.11 (0.39), residues: 531 helix: 1.16 (0.39), residues: 209 sheet: -0.38 (0.70), residues: 67 loop : -0.67 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.006 0.001 TYR A 357 PHE 0.008 0.001 PHE A 358 TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 5687) covalent geometry : angle 0.51775 / 0.26 ( 7918) hydrogen bonds : bond 0.03200 / 2.15 ( 216) hydrogen bonds : angle 3.91639 / 2.81 ( 553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7909 (OUTLIER) cc_final: 0.7192 (p0) REVERT: A 31 LEU cc_start: 0.9053 (tp) cc_final: 0.8691 (tp) REVERT: A 43 MET cc_start: 0.9143 (mmm) cc_final: 0.8872 (mmm) REVERT: A 53 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.9045 (tpm170) REVERT: A 117 MET cc_start: 0.8359 (ptp) cc_final: 0.7810 (ptt) REVERT: A 143 GLU cc_start: 0.7793 (mp0) cc_final: 0.7295 (mp0) REVERT: A 224 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.7020 (mp) REVERT: A 355 LYS cc_start: 0.9630 (tppt) cc_final: 0.9300 (mttt) REVERT: A 632 MET cc_start: 0.8715 (ppp) cc_final: 0.8365 (ppp) outliers start: 19 outliers final: 14 residues processed: 55 average time/residue: 0.0694 time to fit residues: 5.2852 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 4 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.109285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.080940 restraints weight = 20353.813| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 5.35 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5687 Z= 0.099 Angle : 0.534 13.139 7918 Z= 0.263 Chirality : 0.036 0.137 926 Planarity : 0.004 0.048 820 Dihedral : 15.596 75.429 1395 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.45 % Allowed : 24.34 % Favored : 72.21 % 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: 0.09 (0.39), residues: 531 helix: 1.14 (0.39), residues: 210 sheet: -0.34 (0.70), residues: 67 loop : -0.70 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.020 0.001 TYR A 217 PHE 0.009 0.001 PHE A 358 TRP 0.001 0.000 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 5687) covalent geometry : angle 0.53378 / 0.26 ( 7918) hydrogen bonds : bond 0.03181 / 2.15 ( 216) hydrogen bonds : angle 3.88285 / 2.80 ( 553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8295 (mmm) cc_final: 0.8053 (mmm) REVERT: A 26 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7150 (p0) REVERT: A 31 LEU cc_start: 0.9056 (tp) cc_final: 0.8697 (tp) REVERT: A 43 MET cc_start: 0.9146 (mmm) cc_final: 0.8876 (mmm) REVERT: A 53 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9024 (tpm170) REVERT: A 117 MET cc_start: 0.8328 (ptp) cc_final: 0.7809 (ptt) REVERT: A 143 GLU cc_start: 0.7779 (mp0) cc_final: 0.7250 (mp0) REVERT: A 224 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7019 (mp) REVERT: A 355 LYS cc_start: 0.9632 (tppt) cc_final: 0.9296 (mttt) REVERT: A 632 MET cc_start: 0.8700 (ppp) cc_final: 0.8345 (ppp) outliers start: 17 outliers final: 14 residues processed: 54 average time/residue: 0.0710 time to fit residues: 5.2683 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASN Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.108546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.080182 restraints weight = 20369.239| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 5.44 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5687 Z= 0.110 Angle : 0.542 11.551 7918 Z= 0.271 Chirality : 0.036 0.160 926 Planarity : 0.004 0.049 820 Dihedral : 15.598 75.469 1395 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.25 % Allowed : 24.95 % Favored : 71.81 % 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 (0.39), residues: 531 helix: 1.22 (0.39), residues: 209 sheet: -0.33 (0.69), residues: 67 loop : -0.68 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.006 0.001 TYR A 357 PHE 0.008 0.001 PHE A 358 TRP 0.003 0.001 TRP A 100 HIS 0.002 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5687) covalent geometry : angle 0.54213 / 0.27 ( 7918) hydrogen bonds : bond 0.03347 / 2.28 ( 216) hydrogen bonds : angle 3.91996 / 2.81 ( 553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1288.19 seconds wall clock time: 22 minutes 53.31 seconds (1373.31 seconds total)