Starting phenix.real_space_refine on Tue Aug 4 19:42:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.map" model { file = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k88_36947/08_2026/8k88_36947.cif" } resolution = 2.6 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= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 44 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4124 2.51 5 N 1150 2.21 5 O 1345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 6686 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 444 Classifications: {'DNA': 1, 'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "A" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 439} Chain: "B" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2053 Classifications: {'peptide': 258} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 247} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.25 Number of scatterers: 6686 At special positions: 0 Unit cell: (74.6512, 90.2876, 107.437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 44 15.00 Mg 1 11.99 O 1345 8.00 N 1150 7.00 C 4124 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: 0.61 Conformation dependent library (CDL) restraints added in 329.4 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.7% alpha, 24.1% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.883A pdb=" N CYS A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.735A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.949A pdb=" N GLY A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.705A pdb=" N ARG A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 4.920A pdb=" N LYS A 156 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.891A pdb=" N LEU A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 209 removed outlier: 3.680A pdb=" N VAL A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 295 Processing helix chain 'A' and resid 312 through 323 removed outlier: 3.634A pdb=" N PHE A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 4.266A pdb=" N THR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.024A pdb=" N VAL A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'B' and resid 355 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.601A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 513 through 519 removed outlier: 4.968A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 6.156A pdb=" N LEU A 331 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 223 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N HIS A 306 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 225 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.324A pdb=" N CYS A 107 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 54 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.190A pdb=" N ARG A 51 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 147 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 53 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 149 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 55 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 146 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE A 183 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 148 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 3.624A pdb=" N ALA A 355 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA8, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.262A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 374 removed outlier: 3.739A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 382 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 11.045A pdb=" N ARG B 344 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 343 " --> pdb=" O TYR B 403 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR B 403 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N CYS B 345 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN B 401 " --> pdb=" O CYS B 345 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 347 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 399 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 349 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 556 through 561 271 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1887 1.34 - 1.45: 1374 1.45 - 1.57: 3555 1.57 - 1.69: 86 1.69 - 1.81: 32 Bond restraints: 6934 Sorted by residual: bond pdb=" C3' DA C 15 " pdb=" C2' DA C 15 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DT C 23 " pdb=" C2' DT C 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.82e+00 bond pdb=" C3' DC C 20 " pdb=" C2' DC C 20 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.39e+00 bond pdb=" C3' DC C 21 " pdb=" C2' DC C 21 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.34e+00 bond pdb=" C3' DC C 9 " pdb=" C2' DC C 9 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.14e+00 ... (remaining 6929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 9317 1.78 - 3.55: 249 3.55 - 5.33: 20 5.33 - 7.10: 6 7.10 - 8.88: 2 Bond angle restraints: 9594 Sorted by residual: angle pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sigma weight residual 117.70 123.50 -5.80 1.20e+00 6.94e-01 2.34e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT C 24 " pdb=" C4 DT C 24 " pdb=" O4 DT C 24 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 13 " pdb=" C4 DT C 13 " pdb=" O4 DT C 13 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" C1' G D 15 " pdb=" N9 G D 15 " pdb=" C4 G D 15 " ideal model delta sigma weight residual 126.50 131.84 -5.34 1.30e+00 5.92e-01 1.69e+01 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 3828 34.39 - 68.77: 273 68.77 - 103.16: 14 103.16 - 137.54: 1 137.54 - 171.93: 1 Dihedral angle restraints: 4117 sinusoidal: 2007 harmonic: 2110 Sorted by residual: dihedral pdb=" O4' U D 2 " pdb=" C1' U D 2 " pdb=" N1 U D 2 " pdb=" C2 U D 2 " ideal model delta sinusoidal sigma weight residual -160.00 11.93 -171.93 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " pdb=" NE ARG A 69 " pdb=" CZ ARG A 69 " ideal model delta sinusoidal sigma weight residual -90.00 -37.10 -52.90 2 1.50e+01 4.44e-03 1.36e+01 dihedral pdb=" C4' DT C 13 " pdb=" C3' DT C 13 " pdb=" O3' DT C 13 " pdb=" P DA C 14 " ideal model delta sinusoidal sigma weight residual 220.00 103.43 116.57 1 3.50e+01 8.16e-04 1.13e+01 ... (remaining 4114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 696 0.032 - 0.064: 243 0.064 - 0.096: 65 0.096 - 0.128: 59 0.128 - 0.160: 11 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C3' DT C 24 " pdb=" C4' DT C 24 " pdb=" O3' DT C 24 " pdb=" C2' DT C 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" C1' G D 15 " pdb=" O4' G D 15 " pdb=" C2' G D 15 " pdb=" N9 G D 15 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1071 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 389 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO A 390 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.68e+00 pdb=" N9 A D 4 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 401 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 402 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.029 5.00e-02 4.00e+02 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 44 2.56 - 3.14: 4837 3.14 - 3.73: 10670 3.73 - 4.31: 15184 4.31 - 4.90: 24623 Nonbonded interactions: 55358 Sorted by model distance: nonbonded pdb=" OXT MET A 473 " pdb="MG MG A 501 " model vdw 1.973 2.170 nonbonded pdb=" OP1 A D 3 " pdb="MG MG A 501 " model vdw 1.987 2.170 nonbonded pdb=" OP2 A D 1 " pdb="MG MG A 501 " model vdw 2.070 2.170 nonbonded pdb=" O THR A 242 " pdb=" OG1 THR A 262 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN A 195 " pdb=" ND2 ASN A 436 " model vdw 2.212 3.120 ... (remaining 55353 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: 1.730 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.003 0.034 6934 Z= 0.234 Angle : 0.634 8.877 9594 Z= 0.445 Chirality : 0.044 0.160 1074 Planarity : 0.005 0.065 1076 Dihedral : 20.288 171.926 2761 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.96 % Allowed : 27.97 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.32), residues: 722 helix: 2.27 (0.35), residues: 221 sheet: 0.96 (0.40), residues: 180 loop : 0.16 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 529 TYR 0.022 0.001 TYR A 341 PHE 0.008 0.001 PHE A 137 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.23 ( 6934) covalent geometry : angle 0.63358 / 0.44 ( 9594) hydrogen bonds : bond 0.14900 / 15.94 ( 297) hydrogen bonds : angle 6.07695 / 7.33 ( 811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.200 Fit side-chains REVERT: A 156 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8197 (ptmm) outliers start: 6 outliers final: 3 residues processed: 193 average time/residue: 0.6241 time to fit residues: 125.3450 Evaluate side-chains 188 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 GLN A 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106775 restraints weight = 9150.370| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.57 r_work: 0.3347 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6934 Z= 0.144 Angle : 0.551 6.873 9594 Z= 0.305 Chirality : 0.042 0.174 1074 Planarity : 0.005 0.051 1076 Dihedral : 18.471 173.762 1379 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.57 % Allowed : 25.24 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.32), residues: 722 helix: 2.38 (0.35), residues: 222 sheet: 0.89 (0.40), residues: 180 loop : 0.09 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 529 TYR 0.014 0.001 TYR A 341 PHE 0.016 0.001 PHE A 304 TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6934) covalent geometry : angle 0.55150 / 0.31 ( 9594) hydrogen bonds : bond 0.04390 / 5.01 ( 297) hydrogen bonds : angle 4.60978 / 5.59 ( 811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.275 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 192 average time/residue: 0.7112 time to fit residues: 141.9801 Evaluate side-chains 193 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.118799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107367 restraints weight = 9004.085| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.58 r_work: 0.3357 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6934 Z= 0.116 Angle : 0.511 6.309 9594 Z= 0.286 Chirality : 0.040 0.163 1074 Planarity : 0.005 0.044 1076 Dihedral : 18.448 173.198 1371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.38 % Allowed : 22.83 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.32), residues: 722 helix: 2.41 (0.35), residues: 222 sheet: 0.90 (0.41), residues: 180 loop : 0.09 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 529 TYR 0.013 0.001 TYR A 366 PHE 0.016 0.001 PHE A 143 TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 6934) covalent geometry : angle 0.51067 / 0.29 ( 9594) hydrogen bonds : bond 0.03920 / 4.52 ( 297) hydrogen bonds : angle 4.34315 / 5.27 ( 811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.216 Fit side-chains REVERT: B 504 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7506 (mmm) outliers start: 21 outliers final: 12 residues processed: 193 average time/residue: 0.6873 time to fit residues: 138.2924 Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.0040 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 HIS A 434 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.119193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107796 restraints weight = 9049.329| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.57 r_work: 0.3359 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6934 Z= 0.111 Angle : 0.498 6.350 9594 Z= 0.278 Chirality : 0.040 0.163 1074 Planarity : 0.004 0.044 1076 Dihedral : 18.364 172.388 1371 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.38 % Allowed : 23.63 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.33), residues: 722 helix: 2.47 (0.35), residues: 222 sheet: 0.90 (0.41), residues: 180 loop : 0.15 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.011 0.001 PHE A 304 TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 6934) covalent geometry : angle 0.49796 / 0.28 ( 9594) hydrogen bonds : bond 0.03611 / 4.18 ( 297) hydrogen bonds : angle 4.21862 / 5.14 ( 811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.250 Fit side-chains REVERT: B 358 GLU cc_start: 0.7922 (tp30) cc_final: 0.7709 (tp30) REVERT: B 504 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7518 (mmm) outliers start: 21 outliers final: 11 residues processed: 193 average time/residue: 0.6800 time to fit residues: 136.6687 Evaluate side-chains 199 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107526 restraints weight = 9148.528| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.58 r_work: 0.3351 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6934 Z= 0.115 Angle : 0.495 6.288 9594 Z= 0.276 Chirality : 0.040 0.163 1074 Planarity : 0.004 0.047 1076 Dihedral : 18.304 170.421 1371 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.86 % Allowed : 23.47 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.33), residues: 722 helix: 2.51 (0.35), residues: 222 sheet: 0.88 (0.41), residues: 180 loop : 0.10 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 69 TYR 0.013 0.001 TYR A 366 PHE 0.010 0.001 PHE B 391 TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 6934) covalent geometry : angle 0.49529 / 0.28 ( 9594) hydrogen bonds : bond 0.03535 / 4.10 ( 297) hydrogen bonds : angle 4.15771 / 5.03 ( 811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.262 Fit side-chains REVERT: B 358 GLU cc_start: 0.7934 (tp30) cc_final: 0.7720 (tp30) REVERT: B 504 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7550 (mmm) outliers start: 24 outliers final: 13 residues processed: 193 average time/residue: 0.7313 time to fit residues: 146.8568 Evaluate side-chains 195 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107168 restraints weight = 9163.254| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.57 r_work: 0.3347 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6934 Z= 0.128 Angle : 0.497 6.251 9594 Z= 0.277 Chirality : 0.040 0.165 1074 Planarity : 0.004 0.046 1076 Dihedral : 18.234 166.264 1371 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.38 % Allowed : 23.79 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.33), residues: 722 helix: 2.51 (0.35), residues: 222 sheet: 0.81 (0.41), residues: 180 loop : 0.10 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.010 0.001 PHE B 391 TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 6934) covalent geometry : angle 0.49747 / 0.28 ( 9594) hydrogen bonds : bond 0.03550 / 4.10 ( 297) hydrogen bonds : angle 4.15286 / 5.04 ( 811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.243 Fit side-chains REVERT: A 55 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8509 (tt) REVERT: B 358 GLU cc_start: 0.7929 (tp30) cc_final: 0.7723 (tp30) REVERT: B 504 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7547 (mmm) outliers start: 21 outliers final: 12 residues processed: 190 average time/residue: 0.6375 time to fit residues: 126.1094 Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.118610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107085 restraints weight = 9080.475| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.57 r_work: 0.3349 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6934 Z= 0.132 Angle : 0.506 6.224 9594 Z= 0.280 Chirality : 0.040 0.166 1074 Planarity : 0.004 0.044 1076 Dihedral : 18.227 166.573 1371 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.54 % Allowed : 23.63 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.33), residues: 722 helix: 2.51 (0.35), residues: 222 sheet: 0.84 (0.41), residues: 180 loop : 0.09 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.010 0.001 PHE A 304 TRP 0.007 0.001 TRP B 502 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 6934) covalent geometry : angle 0.50566 / 0.28 ( 9594) hydrogen bonds : bond 0.03571 / 4.13 ( 297) hydrogen bonds : angle 4.14193 / 5.03 ( 811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.246 Fit side-chains REVERT: A 55 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8512 (tt) REVERT: B 358 GLU cc_start: 0.7933 (tp30) cc_final: 0.7730 (tp30) REVERT: B 504 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7550 (mmm) outliers start: 22 outliers final: 11 residues processed: 185 average time/residue: 0.6914 time to fit residues: 133.2881 Evaluate side-chains 199 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 504 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104179 restraints weight = 9029.171| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.56 r_work: 0.3304 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6934 Z= 0.230 Angle : 0.565 6.698 9594 Z= 0.307 Chirality : 0.043 0.200 1074 Planarity : 0.005 0.048 1076 Dihedral : 18.317 170.380 1371 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.57 % Allowed : 24.76 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.32), residues: 722 helix: 2.35 (0.35), residues: 222 sheet: 0.78 (0.41), residues: 180 loop : -0.00 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.022 0.002 TYR A 341 PHE 0.013 0.002 PHE A 304 TRP 0.009 0.001 TRP B 502 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 6934) covalent geometry : angle 0.56512 / 0.31 ( 9594) hydrogen bonds : bond 0.04232 / 4.80 ( 297) hydrogen bonds : angle 4.29570 / 5.21 ( 811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.259 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 190 average time/residue: 0.6851 time to fit residues: 135.6878 Evaluate side-chains 186 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 483 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105706 restraints weight = 9118.502| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.55 r_work: 0.3327 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6934 Z= 0.141 Angle : 0.533 6.006 9594 Z= 0.294 Chirality : 0.041 0.164 1074 Planarity : 0.005 0.045 1076 Dihedral : 18.337 170.024 1371 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.09 % Allowed : 25.08 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.32), residues: 722 helix: 2.39 (0.35), residues: 222 sheet: 0.75 (0.41), residues: 180 loop : 0.02 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.014 0.001 TYR A 366 PHE 0.018 0.001 PHE A 257 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6934) covalent geometry : angle 0.53279 / 0.29 ( 9594) hydrogen bonds : bond 0.03815 / 4.41 ( 297) hydrogen bonds : angle 4.22565 / 5.12 ( 811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.247 Fit side-chains REVERT: A 14 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8511 (mm) outliers start: 13 outliers final: 10 residues processed: 182 average time/residue: 0.6145 time to fit residues: 116.3526 Evaluate side-chains 197 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104806 restraints weight = 9150.774| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.58 r_work: 0.3314 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6934 Z= 0.183 Angle : 0.549 6.462 9594 Z= 0.300 Chirality : 0.042 0.179 1074 Planarity : 0.005 0.044 1076 Dihedral : 18.322 170.928 1371 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 26.05 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.32), residues: 722 helix: 2.33 (0.35), residues: 222 sheet: 0.73 (0.41), residues: 180 loop : -0.03 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.016 0.001 TYR A 341 PHE 0.024 0.001 PHE A 257 TRP 0.009 0.001 TRP B 502 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 6934) covalent geometry : angle 0.54928 / 0.30 ( 9594) hydrogen bonds : bond 0.03948 / 4.51 ( 297) hydrogen bonds : angle 4.24865 / 5.15 ( 811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.259 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 186 average time/residue: 0.6309 time to fit residues: 122.3053 Evaluate side-chains 192 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 411 ARG Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105217 restraints weight = 9075.448| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.55 r_work: 0.3323 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6934 Z= 0.157 Angle : 0.543 6.478 9594 Z= 0.299 Chirality : 0.042 0.172 1074 Planarity : 0.005 0.043 1076 Dihedral : 18.336 171.108 1371 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.45 % Allowed : 26.53 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.32), residues: 722 helix: 2.34 (0.35), residues: 222 sheet: 0.73 (0.41), residues: 180 loop : -0.03 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 69 TYR 0.014 0.001 TYR A 341 PHE 0.029 0.001 PHE A 257 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 6934) covalent geometry : angle 0.54270 / 0.30 ( 9594) hydrogen bonds : bond 0.03864 / 4.44 ( 297) hydrogen bonds : angle 4.23345 / 5.13 ( 811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.75 seconds wall clock time: 55 minutes 20.77 seconds (3320.77 seconds total)