Starting phenix.real_space_refine on Thu Jul 2 01:42:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw6_48678/07_2026/9mw6_48678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw6_48678/07_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_48678/07_2026/9mw6_48678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw6_48678/07_2026/9mw6_48678.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw6_48678/07_2026/9mw6_48678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw6_48678/07_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-dev-6108/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: 1.58, per 1000 atoms: 0.29 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: 0.51 Conformation dependent library (CDL) restraints added in 167.1 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: 0.67 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: 1.11 Time building geometry restraints manager: 0.69 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: 7854 2.37 - 4.73: 53 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: 756 0.047 - 0.094: 136 0.094 - 0.141: 33 0.141 - 0.188: 0 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=" CA ILE A 454 " pdb=" N ILE A 454 " pdb=" C ILE A 454 " pdb=" CB ILE A 454 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" C PRO A 152 " pdb=" CB PRO A 152 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.51e-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: 3.660 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.240 ------------------------------------------------------------------------------- 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= 0.199 Angle : 0.619 11.827 7918 Z= 0.373 Chirality : 0.038 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 0.00351 / 0.20 ( 5687) covalent geometry : angle 0.61906 / 0.37 ( 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 : 0.199 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: 0.0717 time to fit residues: 5.2310 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 : 0.188 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.4190 r_free = 0.4190 target = 0.107180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.078451 restraints weight = 20678.814| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.45 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5687 Z= 0.141 Angle : 0.548 7.639 7918 Z= 0.292 Chirality : 0.038 0.139 926 Planarity : 0.004 0.048 820 Dihedral : 15.886 75.880 1415 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.85 % Allowed : 21.10 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.38), residues: 531 helix: 1.07 (0.38), residues: 204 sheet: -0.33 (0.61), residues: 85 loop : -1.02 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.009 0.001 TYR A 560 PHE 0.012 0.001 PHE A 530 TRP 0.005 0.001 TRP A 100 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 5687) covalent geometry : angle 0.54818 / 0.29 ( 7918) hydrogen bonds : bond 0.04754 / 3.24 ( 216) hydrogen bonds : angle 4.59879 / 3.30 ( 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 63 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8164 (mmt) cc_final: 0.7870 (mmm) REVERT: A 31 LEU cc_start: 0.9035 (tp) cc_final: 0.8665 (tp) REVERT: A 43 MET cc_start: 0.9179 (mmm) cc_final: 0.8933 (mmm) REVERT: A 117 MET cc_start: 0.8583 (ptp) cc_final: 0.8007 (ptt) REVERT: A 143 GLU cc_start: 0.7778 (mp0) cc_final: 0.7241 (mp0) REVERT: A 224 ILE cc_start: 0.7136 (mp) cc_final: 0.6895 (mp) REVERT: A 632 MET cc_start: 0.8713 (ppp) cc_final: 0.8418 (ppp) outliers start: 19 outliers final: 12 residues processed: 60 average time/residue: 0.0525 time to fit residues: 4.7766 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 : 0.200 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.106034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.077628 restraints weight = 20327.143| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 5.33 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5687 Z= 0.157 Angle : 0.546 6.420 7918 Z= 0.291 Chirality : 0.038 0.142 926 Planarity : 0.004 0.049 820 Dihedral : 15.658 76.065 1399 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.85 % Allowed : 21.91 % Favored : 74.24 % 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: 1.16 (0.38), residues: 203 sheet: -0.45 (0.65), residues: 74 loop : -0.85 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.015 0.001 TYR A 217 PHE 0.013 0.002 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 0.00336 / 0.16 ( 5687) covalent geometry : angle 0.54555 / 0.29 ( 7918) hydrogen bonds : bond 0.04576 / 3.14 ( 216) hydrogen bonds : angle 4.44257 / 3.22 ( 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 65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8198 (mmt) cc_final: 0.7923 (mmm) REVERT: A 31 LEU cc_start: 0.9047 (tp) cc_final: 0.8713 (tp) REVERT: A 43 MET cc_start: 0.9200 (mmm) cc_final: 0.8939 (mmm) REVERT: A 117 MET cc_start: 0.8584 (ptp) cc_final: 0.8001 (ptt) REVERT: A 143 GLU cc_start: 0.7800 (mp0) cc_final: 0.7274 (mp0) REVERT: A 224 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6954 (mp) REVERT: A 355 LYS cc_start: 0.9643 (tppt) cc_final: 0.9307 (mttt) REVERT: A 384 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8115 (t80) REVERT: A 448 VAL cc_start: 0.7751 (m) cc_final: 0.7370 (p) REVERT: A 550 MET cc_start: 0.9145 (tmm) cc_final: 0.8792 (tpp) REVERT: A 632 MET cc_start: 0.8708 (ppp) cc_final: 0.8400 (ppp) outliers start: 19 outliers final: 12 residues processed: 62 average time/residue: 0.0564 time to fit residues: 5.0825 Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 175 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 195 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 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: 2.9990 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 41 optimal weight: 10.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.107323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.078737 restraints weight = 20250.765| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 5.34 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 5687 Z= 0.108 Angle : 0.521 7.072 7918 Z= 0.272 Chirality : 0.037 0.138 926 Planarity : 0.004 0.046 820 Dihedral : 15.611 75.836 1397 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.04 % Allowed : 23.94 % Favored : 73.02 % 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: -0.03 (0.38), residues: 531 helix: 1.15 (0.38), residues: 203 sheet: -0.69 (0.67), residues: 69 loop : -0.74 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.006 0.001 TYR A 357 PHE 0.009 0.001 PHE A 358 TRP 0.001 0.001 TRP A 100 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 5687) covalent geometry : angle 0.52094 / 0.27 ( 7918) hydrogen bonds : bond 0.03784 / 2.55 ( 216) hydrogen bonds : angle 4.23070 / 3.06 ( 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 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8231 (mmt) cc_final: 0.7963 (mmm) REVERT: A 31 LEU cc_start: 0.9075 (tp) cc_final: 0.8705 (tp) REVERT: A 43 MET cc_start: 0.9172 (mmm) cc_final: 0.8909 (mmm) REVERT: A 117 MET cc_start: 0.8528 (ptp) cc_final: 0.7952 (ptt) REVERT: A 143 GLU cc_start: 0.7750 (mp0) cc_final: 0.7242 (mp0) REVERT: A 224 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6953 (mp) REVERT: A 355 LYS cc_start: 0.9636 (tppt) cc_final: 0.9301 (mttt) REVERT: A 384 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.8121 (t80) REVERT: A 501 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8968 (m-30) REVERT: A 632 MET cc_start: 0.8711 (ppp) cc_final: 0.8385 (ppp) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.0478 time to fit residues: 3.9328 Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 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: 4.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.104443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.076044 restraints weight = 20931.870| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 5.38 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5687 Z= 0.196 Angle : 0.574 7.110 7918 Z= 0.305 Chirality : 0.039 0.145 926 Planarity : 0.004 0.051 820 Dihedral : 15.618 76.103 1395 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.07 % Allowed : 22.92 % 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: -0.29 (0.38), residues: 531 helix: 0.88 (0.37), residues: 210 sheet: -0.75 (0.73), residues: 59 loop : -0.91 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 478 TYR 0.014 0.002 TYR A 217 PHE 0.014 0.002 PHE A 530 TRP 0.007 0.001 TRP A 100 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 ( 5687) covalent geometry : angle 0.57358 / 0.30 ( 7918) hydrogen bonds : bond 0.05282 / 3.68 ( 216) hydrogen bonds : angle 4.37051 / 3.18 ( 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 70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9049 (tp) cc_final: 0.8718 (tp) REVERT: A 43 MET cc_start: 0.9196 (mmm) cc_final: 0.8953 (mmm) REVERT: A 117 MET cc_start: 0.8638 (ptp) cc_final: 0.8045 (ptt) REVERT: A 143 GLU cc_start: 0.7790 (mp0) cc_final: 0.7265 (mp0) REVERT: A 355 LYS cc_start: 0.9649 (tppt) cc_final: 0.9303 (mttt) REVERT: A 384 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7870 (t80) REVERT: A 448 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7425 (p) REVERT: A 501 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.9036 (m-30) REVERT: A 632 MET cc_start: 0.8748 (ppp) cc_final: 0.8355 (ppp) outliers start: 25 outliers final: 14 residues processed: 64 average time/residue: 0.0604 time to fit residues: 5.5480 Evaluate side-chains 61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 99 SER 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 175 THR Chi-restraints excluded: chain A residue 196 GLU 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 448 VAL Chi-restraints excluded: chain A residue 501 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.106910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078376 restraints weight = 20556.976| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 5.42 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1253 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= 0.113 Angle : 0.529 9.680 7918 Z= 0.274 Chirality : 0.037 0.137 926 Planarity : 0.004 0.049 820 Dihedral : 15.593 75.978 1395 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.85 % Allowed : 25.15 % Favored : 70.99 % 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: 0.94 (0.38), residues: 209 sheet: -0.62 (0.75), residues: 57 loop : -0.80 (0.40), residues: 265 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 0.010 0.001 PHE A 527 TRP 0.001 0.001 TRP A 100 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 5687) covalent geometry : angle 0.52927 / 0.27 ( 7918) hydrogen bonds : bond 0.03839 / 2.60 ( 216) hydrogen bonds : angle 4.14539 / 3.00 ( 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 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7201 (p0) REVERT: A 31 LEU cc_start: 0.9086 (tp) cc_final: 0.8716 (tp) REVERT: A 43 MET cc_start: 0.9167 (mmm) cc_final: 0.8911 (mmm) REVERT: A 53 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9107 (tpm170) REVERT: A 117 MET cc_start: 0.8546 (ptp) cc_final: 0.7941 (ptt) REVERT: A 143 GLU cc_start: 0.7830 (mp0) cc_final: 0.7323 (mp0) REVERT: A 355 LYS cc_start: 0.9643 (tppt) cc_final: 0.9302 (mttt) REVERT: A 384 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 632 MET cc_start: 0.8733 (ppp) cc_final: 0.8320 (ppp) outliers start: 19 outliers final: 13 residues processed: 59 average time/residue: 0.0611 time to fit residues: 5.1283 Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 196 GLU Chi-restraints excluded: chain A residue 360 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.106468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.078026 restraints weight = 20703.154| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 5.45 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5687 Z= 0.136 Angle : 0.534 7.645 7918 Z= 0.277 Chirality : 0.038 0.138 926 Planarity : 0.004 0.050 820 Dihedral : 15.585 75.928 1395 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.85 % Allowed : 25.96 % Favored : 70.18 % 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: -0.18 (0.38), residues: 531 helix: 0.95 (0.38), residues: 209 sheet: -0.65 (0.75), residues: 57 loop : -0.84 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 53 TYR 0.007 0.001 TYR A 357 PHE 0.011 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 0.00294 / 0.14 ( 5687) covalent geometry : angle 0.53439 / 0.28 ( 7918) hydrogen bonds : bond 0.04003 / 2.75 ( 216) hydrogen bonds : angle 4.12077 / 2.98 ( 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 63 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9075 (tp) cc_final: 0.8744 (tp) REVERT: A 43 MET cc_start: 0.9175 (mmm) cc_final: 0.8913 (mmm) REVERT: A 53 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9094 (tpm170) REVERT: A 117 MET cc_start: 0.8542 (ptp) cc_final: 0.7966 (ptt) REVERT: A 143 GLU cc_start: 0.7801 (mp0) cc_final: 0.7327 (mp0) REVERT: A 355 LYS cc_start: 0.9641 (tppt) cc_final: 0.9306 (mttt) REVERT: A 384 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 632 MET cc_start: 0.8735 (ppp) cc_final: 0.8318 (ppp) outliers start: 19 outliers final: 14 residues processed: 60 average time/residue: 0.0707 time to fit residues: 5.8661 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG 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 195 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 360 ASN 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 556 LEU Chi-restraints excluded: chain A residue 602 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: 0.7980 chunk 48 optimal weight: 0.0070 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.108147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079587 restraints weight = 20241.288| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 5.48 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5687 Z= 0.102 Angle : 0.543 10.498 7918 Z= 0.274 Chirality : 0.037 0.145 926 Planarity : 0.004 0.050 820 Dihedral : 15.574 75.720 1395 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.04 % Allowed : 26.77 % Favored : 70.18 % 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: 0.98 (0.38), residues: 210 sheet: -0.54 (0.75), residues: 57 loop : -0.88 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 603 TYR 0.018 0.002 TYR A 217 PHE 0.008 0.001 PHE A 358 TRP 0.001 0.000 TRP A 105 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 5687) covalent geometry : angle 0.54281 / 0.27 ( 7918) hydrogen bonds : bond 0.03255 / 2.17 ( 216) hydrogen bonds : angle 3.97881 / 2.85 ( 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 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7122 (p0) REVERT: A 31 LEU cc_start: 0.9095 (tp) cc_final: 0.8732 (tp) REVERT: A 43 MET cc_start: 0.9165 (mmm) cc_final: 0.8903 (mmm) REVERT: A 53 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.9115 (tpm170) REVERT: A 117 MET cc_start: 0.8450 (ptp) cc_final: 0.7883 (ptt) REVERT: A 143 GLU cc_start: 0.7768 (mp0) cc_final: 0.7314 (mp0) REVERT: A 355 LYS cc_start: 0.9624 (tppt) cc_final: 0.9292 (mttt) REVERT: A 384 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (t80) REVERT: A 632 MET cc_start: 0.8735 (ppp) cc_final: 0.8392 (ppp) outliers start: 15 outliers final: 8 residues processed: 56 average time/residue: 0.0571 time to fit residues: 4.6021 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 : 0.137 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain A residue 123 LEU 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 384 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 602 LEU 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: 0.8980 chunk 21 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.077905 restraints weight = 20871.743| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 5.43 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5687 Z= 0.152 Angle : 0.560 9.104 7918 Z= 0.287 Chirality : 0.038 0.237 926 Planarity : 0.004 0.050 820 Dihedral : 15.575 75.794 1395 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.65 % Allowed : 25.96 % Favored : 70.39 % 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: 1.04 (0.38), residues: 209 sheet: -0.49 (0.75), residues: 57 loop : -0.96 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.007 0.001 TYR A 560 PHE 0.011 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 0.00329 / 0.15 ( 5687) covalent geometry : angle 0.55971 / 0.29 ( 7918) hydrogen bonds : bond 0.04033 / 2.77 ( 216) hydrogen bonds : angle 4.10648 / 2.95 ( 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: 18 poor density : 42 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9067 (tp) cc_final: 0.8737 (tp) REVERT: A 43 MET cc_start: 0.9179 (mmm) cc_final: 0.8918 (mmm) REVERT: A 53 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.9075 (tpm170) REVERT: A 117 MET cc_start: 0.8522 (ptp) cc_final: 0.7961 (ptt) REVERT: A 143 GLU cc_start: 0.7808 (mp0) cc_final: 0.7326 (mp0) REVERT: A 355 LYS cc_start: 0.9629 (tppt) cc_final: 0.9296 (mttt) REVERT: A 384 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.8032 (t80) REVERT: A 632 MET cc_start: 0.8726 (ppp) cc_final: 0.8309 (ppp) outliers start: 18 outliers final: 16 residues processed: 57 average time/residue: 0.0645 time to fit residues: 5.0385 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 : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 53 ARG 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 195 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 431 LEU 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: 0.0870 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.108535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.079101 restraints weight = 20336.191| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 5.59 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1654 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= 0.112 Angle : 0.563 13.495 7918 Z= 0.279 Chirality : 0.037 0.137 926 Planarity : 0.004 0.049 820 Dihedral : 15.569 75.759 1395 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.25 % Allowed : 26.17 % Favored : 70.59 % 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: -0.22 (0.38), residues: 531 helix: 0.91 (0.38), residues: 212 sheet: -0.42 (0.75), residues: 57 loop : -0.94 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 603 TYR 0.021 0.001 TYR A 217 PHE 0.008 0.001 PHE A 358 TRP 0.001 0.001 TRP A 100 HIS 0.002 0.000 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 5687) covalent geometry : angle 0.56281 / 0.28 ( 7918) hydrogen bonds : bond 0.03489 / 2.38 ( 216) hydrogen bonds : angle 4.00439 / 2.89 ( 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 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8327 (mmm) cc_final: 0.8088 (mmm) REVERT: A 31 LEU cc_start: 0.9059 (tp) cc_final: 0.8696 (tp) REVERT: A 43 MET cc_start: 0.9157 (mmm) cc_final: 0.8898 (mmm) REVERT: A 53 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.9104 (tpm170) REVERT: A 117 MET cc_start: 0.8493 (ptp) cc_final: 0.7932 (ptt) REVERT: A 143 GLU cc_start: 0.7824 (mp0) cc_final: 0.7372 (mp0) REVERT: A 355 LYS cc_start: 0.9622 (tppt) cc_final: 0.9299 (mttt) REVERT: A 632 MET cc_start: 0.8749 (ppp) cc_final: 0.8405 (ppp) outliers start: 16 outliers final: 15 residues processed: 55 average time/residue: 0.0652 time to fit residues: 5.0039 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 53 ARG 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 195 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 490 VAL 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: 0.9980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.107835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.079540 restraints weight = 20566.160| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 5.48 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1757 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= 0.107 Angle : 0.562 11.363 7918 Z= 0.280 Chirality : 0.037 0.137 926 Planarity : 0.004 0.048 820 Dihedral : 15.566 75.651 1395 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.04 % Allowed : 26.98 % Favored : 69.98 % 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 (0.38), residues: 531 helix: 1.01 (0.38), residues: 211 sheet: -0.35 (0.75), residues: 57 loop : -0.88 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 53 TYR 0.005 0.001 TYR A 505 PHE 0.008 0.001 PHE A 358 TRP 0.001 0.000 TRP A 100 HIS 0.002 0.000 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5687) covalent geometry : angle 0.56197 / 0.28 ( 7918) hydrogen bonds : bond 0.03337 / 2.27 ( 216) hydrogen bonds : angle 3.97143 / 2.85 ( 553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.79 seconds wall clock time: 23 minutes 15.92 seconds (1395.92 seconds total)