Starting phenix.real_space_refine on Thu Jul 2 04:57:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.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 { model { file = "/net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga5_29890/07_2026/8ga5_29890.map" } 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= 0.002 sd= 0.091 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 S 42 5.16 5 Cl 6 4.86 5 C 4432 2.51 5 N 1140 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 6789 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3377 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3377 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 3} Chain breaks: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 3} Chain breaks: 3 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.53, per 1000 atoms: 0.23 Number of scatterers: 6789 At special positions: 0 Unit cell: (75.9, 71.775, 112.2, 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) Cl 6 17.00 S 42 16.00 O 1169 8.00 N 1140 7.00 C 4432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 450 " distance=2.02 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS B 25 " distance=2.02 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: 0.76 Conformation dependent library (CDL) restraints added in 358.7 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 81.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.635A pdb=" N CYS A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 71 removed outlier: 3.964A pdb=" N LEU A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.594A pdb=" N ALA A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 147 through 166 Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.584A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 removed outlier: 3.571A pdb=" N ILE A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 4.121A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 285 removed outlier: 4.000A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.966A pdb=" N VAL A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.826A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.571A pdb=" N SER A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.576A pdb=" N ALA A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 Processing helix chain 'A' and resid 356 through 379 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.520A pdb=" N ALA A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.519A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 33 through 71 removed outlier: 3.531A pdb=" N VAL B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.813A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 123 through 140 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 147 through 166 Processing helix chain 'B' and resid 170 through 189 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.847A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 3.722A pdb=" N LYS B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 285 removed outlier: 4.030A pdb=" N TYR B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.507A pdb=" N ARG B 282 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 305 Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.594A pdb=" N SER B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 removed outlier: 4.193A pdb=" N ILE B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 349 Processing helix chain 'B' and resid 356 through 379 removed outlier: 3.549A pdb=" N VAL B 376 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 383 removed outlier: 3.556A pdb=" N HIS B 383 " --> pdb=" O PRO B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.698A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 443 through 460 508 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1051 1.31 - 1.43: 1785 1.43 - 1.56: 3986 1.56 - 1.68: 0 1.68 - 1.81: 76 Bond restraints: 6898 Sorted by residual: bond pdb=" C LEU B 411 " pdb=" O LEU B 411 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.91e+01 bond pdb=" CA LEU B 411 " pdb=" C LEU B 411 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.27e-02 6.20e+03 1.66e+01 bond pdb=" C ILE B 410 " pdb=" N LEU B 411 " ideal model delta sigma weight residual 1.334 1.290 0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" N LEU B 411 " pdb=" CA LEU B 411 " ideal model delta sigma weight residual 1.459 1.420 0.040 1.19e-02 7.06e+03 1.10e+01 bond pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " ideal model delta sigma weight residual 1.529 1.505 0.024 1.55e-02 4.16e+03 2.37e+00 ... (remaining 6893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9063 1.99 - 3.99: 243 3.99 - 5.98: 38 5.98 - 7.97: 15 7.97 - 9.97: 1 Bond angle restraints: 9360 Sorted by residual: angle pdb=" C LEU A 319 " pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 120.24 124.21 -3.97 6.30e-01 2.52e+00 3.96e+01 angle pdb=" N VAL B 241 " pdb=" CA VAL B 241 " pdb=" C VAL B 241 " ideal model delta sigma weight residual 110.05 106.92 3.13 1.09e+00 8.42e-01 8.24e+00 angle pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " pdb=" CG LEU B 411 " ideal model delta sigma weight residual 116.30 126.27 -9.97 3.50e+00 8.16e-02 8.11e+00 angle pdb=" N TYR A 75 " pdb=" CA TYR A 75 " pdb=" C TYR A 75 " ideal model delta sigma weight residual 109.81 115.86 -6.05 2.21e+00 2.05e-01 7.50e+00 angle pdb=" N TYR B 75 " pdb=" CA TYR B 75 " pdb=" C TYR B 75 " ideal model delta sigma weight residual 109.81 115.59 -5.78 2.21e+00 2.05e-01 6.83e+00 ... (remaining 9355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3606 17.66 - 35.31: 354 35.31 - 52.97: 44 52.97 - 70.63: 9 70.63 - 88.28: 3 Dihedral angle restraints: 4016 sinusoidal: 1528 harmonic: 2488 Sorted by residual: dihedral pdb=" CA ASP B 240 " pdb=" C ASP B 240 " pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ALA B 188 " pdb=" C ALA B 188 " pdb=" N ALA B 189 " pdb=" CA ALA B 189 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASP A 240 " pdb=" C ASP A 240 " pdb=" N VAL A 241 " pdb=" CA VAL A 241 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 650 0.037 - 0.074: 346 0.074 - 0.111: 81 0.111 - 0.149: 20 0.149 - 0.186: 3 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA LEU B 411 " pdb=" N LEU B 411 " pdb=" C LEU B 411 " pdb=" CB LEU B 411 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1097 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " 0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 150 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 149 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO B 150 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 358 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO B 359 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 359 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 359 " -0.038 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1970 2.80 - 3.33: 6169 3.33 - 3.85: 12027 3.85 - 4.38: 15075 4.38 - 4.90: 24614 Nonbonded interactions: 59855 Sorted by model distance: nonbonded pdb=" OD2 ASP A 54 " pdb=" O HOH A 601 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.315 3.040 nonbonded pdb=" O LEU A 397 " pdb=" OG SER A 401 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR B 344 " pdb=" O HOH B 601 " model vdw 2.324 3.040 nonbonded pdb=" O ARG A 147 " pdb=" OG1 THR A 151 " model vdw 2.325 3.040 ... (remaining 59850 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.190 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.770 Find NCS groups from input model: 0.080 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:8.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6900 Z= 0.230 Angle : 0.805 9.965 9364 Z= 0.430 Chirality : 0.046 0.186 1100 Planarity : 0.008 0.076 1176 Dihedral : 13.672 88.284 2438 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -5.58 (0.17), residues: 896 helix: -3.85 (0.09), residues: 668 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 340 TYR 0.011 0.002 TYR A 419 PHE 0.015 0.002 PHE B 357 TRP 0.004 0.001 TRP A 253 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 6898) covalent geometry : angle 0.80316 / 0.43 ( 9360) SS BOND : bond 0.00727 / 0.37 ( 2) SS BOND : angle 2.93100 / 1.67 ( 4) hydrogen bonds : bond 0.26359 / 17.47 ( 508) hydrogen bonds : angle 10.30709 / 7.24 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.241 Fit side-chains REVERT: A 17 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6374 (tpt-90) REVERT: B 19 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7243 (mtt-85) REVERT: B 172 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6085 (tm-30) REVERT: B 174 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.8015 (ttm170) REVERT: B 282 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7483 (mtt180) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.6083 time to fit residues: 81.3312 Evaluate side-chains 102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 270 ASN A 284 HIS A 327 ASN A 418 ASN A 460 GLN B 157 ASN B 270 ASN B 284 HIS B 287 ASN B 327 ASN B 418 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100727 restraints weight = 6776.391| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.40 r_work: 0.3026 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6900 Z= 0.171 Angle : 0.589 5.733 9364 Z= 0.296 Chirality : 0.040 0.128 1100 Planarity : 0.006 0.064 1176 Dihedral : 4.687 19.842 960 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 11.36 % Favored : 87.02 % 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: -1.44 (0.24), residues: 896 helix: -0.60 (0.17), residues: 680 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.007 0.001 TYR A 210 PHE 0.024 0.002 PHE B 357 TRP 0.007 0.001 TRP A 291 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 6898) covalent geometry : angle 0.58876 / 0.30 ( 9360) SS BOND : bond 0.00840 / 0.44 ( 2) SS BOND : angle 1.02343 / 0.59 ( 4) hydrogen bonds : bond 0.04749 / 3.17 ( 508) hydrogen bonds : angle 4.79551 / 3.36 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.151 Fit side-chains REVERT: A 15 ARG cc_start: 0.6642 (ttm170) cc_final: 0.6279 (tpt170) REVERT: A 17 ARG cc_start: 0.6186 (ttp80) cc_final: 0.5082 (tpt-90) REVERT: A 205 ARG cc_start: 0.6603 (ttp-110) cc_final: 0.6246 (ttp-110) REVERT: A 276 MET cc_start: 0.8793 (mmm) cc_final: 0.8455 (mmm) REVERT: A 360 MET cc_start: 0.8591 (mtt) cc_final: 0.8346 (mtt) REVERT: B 172 GLU cc_start: 0.6918 (tm-30) cc_final: 0.5713 (tm-30) REVERT: B 174 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7598 (ttm170) REVERT: B 282 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.7019 (mtt180) outliers start: 11 outliers final: 6 residues processed: 107 average time/residue: 0.6737 time to fit residues: 75.1121 Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 293 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101071 restraints weight = 6795.543| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.42 r_work: 0.3027 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6900 Z= 0.146 Angle : 0.531 5.589 9364 Z= 0.265 Chirality : 0.039 0.125 1100 Planarity : 0.005 0.058 1176 Dihedral : 4.401 19.146 960 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 11.36 % Favored : 86.87 % 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: 0.50 (0.27), residues: 896 helix: 0.93 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.007 0.001 TYR B 94 PHE 0.024 0.001 PHE B 357 TRP 0.005 0.001 TRP A 291 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 6898) covalent geometry : angle 0.53061 / 0.26 ( 9360) SS BOND : bond 0.00704 / 0.36 ( 2) SS BOND : angle 1.43053 / 0.84 ( 4) hydrogen bonds : bond 0.04144 / 2.75 ( 508) hydrogen bonds : angle 4.27234 / 3.00 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 15 ARG cc_start: 0.6618 (ttm170) cc_final: 0.6355 (tpt170) REVERT: A 17 ARG cc_start: 0.6189 (ttp80) cc_final: 0.5077 (tpt-90) REVERT: A 20 GLN cc_start: 0.6997 (tm-30) cc_final: 0.5735 (tp40) REVERT: A 205 ARG cc_start: 0.6588 (ttp-110) cc_final: 0.6286 (ttp80) REVERT: A 276 MET cc_start: 0.8792 (mmm) cc_final: 0.8492 (mmm) REVERT: B 172 GLU cc_start: 0.6899 (tm-30) cc_final: 0.5830 (tm-30) REVERT: B 209 ARG cc_start: 0.6761 (mtp-110) cc_final: 0.5424 (mmp80) REVERT: B 245 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 271 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7937 (ptpt) REVERT: B 282 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7031 (mtt180) REVERT: B 385 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7746 (tt0) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 0.6590 time to fit residues: 72.0950 Evaluate side-chains 98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.125554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098529 restraints weight = 6829.238| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.36 r_work: 0.2995 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6900 Z= 0.201 Angle : 0.572 5.397 9364 Z= 0.284 Chirality : 0.042 0.132 1100 Planarity : 0.005 0.059 1176 Dihedral : 4.487 21.884 960 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 13.42 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 896 helix: 1.32 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.010 0.002 TYR A 210 PHE 0.025 0.002 PHE B 357 TRP 0.005 0.001 TRP A 291 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 ( 6898) covalent geometry : angle 0.57081 / 0.28 ( 9360) SS BOND : bond 0.00827 / 0.43 ( 2) SS BOND : angle 1.62962 / 0.95 ( 4) hydrogen bonds : bond 0.04386 / 2.90 ( 508) hydrogen bonds : angle 4.26419 / 2.99 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.217 Fit side-chains REVERT: A 17 ARG cc_start: 0.6205 (ttp80) cc_final: 0.4843 (tpt-90) REVERT: A 21 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5903 (mm) REVERT: A 205 ARG cc_start: 0.6593 (ttp-110) cc_final: 0.6288 (ttp80) REVERT: A 276 MET cc_start: 0.8800 (mmm) cc_final: 0.8435 (mmm) REVERT: B 209 ARG cc_start: 0.6787 (mtp-110) cc_final: 0.5333 (mmp80) REVERT: B 271 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7923 (ptpt) REVERT: B 282 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7023 (mtt180) REVERT: B 385 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7753 (tt0) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 0.6592 time to fit residues: 72.2534 Evaluate side-chains 102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 0.0770 chunk 82 optimal weight: 0.0770 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.129091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101617 restraints weight = 6838.144| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.42 r_work: 0.3035 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6900 Z= 0.125 Angle : 0.502 5.634 9364 Z= 0.249 Chirality : 0.039 0.121 1100 Planarity : 0.004 0.055 1176 Dihedral : 4.196 18.199 960 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.92 % Allowed : 14.31 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 896 helix: 1.81 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.007 0.001 TYR B 94 PHE 0.024 0.001 PHE B 357 TRP 0.003 0.001 TRP B 125 HIS 0.002 0.000 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6898) covalent geometry : angle 0.50172 / 0.25 ( 9360) SS BOND : bond 0.00636 / 0.33 ( 2) SS BOND : angle 1.20911 / 0.71 ( 4) hydrogen bonds : bond 0.03756 / 2.48 ( 508) hydrogen bonds : angle 3.99073 / 2.81 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6252 (ttp80) cc_final: 0.5054 (tpt-90) REVERT: A 20 GLN cc_start: 0.6943 (tm-30) cc_final: 0.5613 (tp40) REVERT: A 30 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6744 (ptpp) REVERT: A 276 MET cc_start: 0.8680 (mmm) cc_final: 0.8384 (mmm) REVERT: B 209 ARG cc_start: 0.6836 (mtp-110) cc_final: 0.5409 (mmp80) REVERT: B 271 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7922 (ptpt) REVERT: B 282 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.6877 (mtt180) REVERT: B 385 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7617 (tt0) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 0.6798 time to fit residues: 72.4357 Evaluate side-chains 92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 56 optimal weight: 0.5980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.127796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100011 restraints weight = 6816.631| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.43 r_work: 0.3013 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6900 Z= 0.154 Angle : 0.526 5.263 9364 Z= 0.261 Chirality : 0.040 0.133 1100 Planarity : 0.004 0.055 1176 Dihedral : 4.225 19.528 960 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.65 % Allowed : 14.01 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.28), residues: 896 helix: 1.89 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.14 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.007 0.001 TYR A 210 PHE 0.028 0.001 PHE B 357 TRP 0.004 0.001 TRP A 291 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6898) covalent geometry : angle 0.52528 / 0.26 ( 9360) SS BOND : bond 0.00782 / 0.41 ( 2) SS BOND : angle 1.26854 / 0.74 ( 4) hydrogen bonds : bond 0.03969 / 2.62 ( 508) hydrogen bonds : angle 4.02341 / 2.83 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6300 (ttp80) cc_final: 0.5098 (tpt-90) REVERT: A 20 GLN cc_start: 0.7006 (tm-30) cc_final: 0.5676 (tp40) REVERT: A 30 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6729 (ptpp) REVERT: A 276 MET cc_start: 0.8775 (mmm) cc_final: 0.8424 (mmm) REVERT: B 20 GLN cc_start: 0.5826 (mm110) cc_final: 0.5272 (tp40) REVERT: B 209 ARG cc_start: 0.6909 (mtp-110) cc_final: 0.5469 (mmp80) REVERT: B 282 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.6913 (mtt180) REVERT: B 385 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7619 (tt0) outliers start: 18 outliers final: 5 residues processed: 105 average time/residue: 0.6673 time to fit residues: 73.3017 Evaluate side-chains 91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 0.0470 chunk 31 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.130389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103020 restraints weight = 6728.335| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.42 r_work: 0.3054 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6900 Z= 0.116 Angle : 0.492 5.407 9364 Z= 0.244 Chirality : 0.038 0.123 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.044 16.760 960 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.77 % Allowed : 14.90 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.28), residues: 896 helix: 2.14 (0.19), residues: 684 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 167 TYR 0.007 0.001 TYR B 94 PHE 0.031 0.001 PHE B 357 TRP 0.003 0.000 TRP B 124 HIS 0.001 0.000 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6898) covalent geometry : angle 0.49108 / 0.24 ( 9360) SS BOND : bond 0.00495 / 0.26 ( 2) SS BOND : angle 1.13258 / 0.66 ( 4) hydrogen bonds : bond 0.03610 / 2.38 ( 508) hydrogen bonds : angle 3.88858 / 2.74 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6309 (ttp80) cc_final: 0.4910 (tpt-90) REVERT: A 20 GLN cc_start: 0.6956 (tm-30) cc_final: 0.5628 (tp40) REVERT: A 21 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5909 (mm) REVERT: B 20 GLN cc_start: 0.5845 (mm110) cc_final: 0.5284 (tp40) REVERT: B 209 ARG cc_start: 0.6846 (mtp-110) cc_final: 0.5434 (mmp80) REVERT: B 282 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.6903 (mtt180) REVERT: B 385 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7529 (tt0) outliers start: 12 outliers final: 4 residues processed: 102 average time/residue: 0.6606 time to fit residues: 70.4688 Evaluate side-chains 94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.126938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099052 restraints weight = 6824.888| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.42 r_work: 0.2999 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6900 Z= 0.178 Angle : 0.553 5.660 9364 Z= 0.273 Chirality : 0.042 0.132 1100 Planarity : 0.004 0.054 1176 Dihedral : 4.256 20.003 960 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.77 % Allowed : 15.04 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.27), residues: 896 helix: 1.99 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.010 0.002 TYR A 210 PHE 0.031 0.002 PHE B 357 TRP 0.005 0.001 TRP A 291 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 6898) covalent geometry : angle 0.55218 / 0.27 ( 9360) SS BOND : bond 0.00781 / 0.40 ( 2) SS BOND : angle 1.39467 / 0.81 ( 4) hydrogen bonds : bond 0.04143 / 2.73 ( 508) hydrogen bonds : angle 4.07922 / 2.87 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6242 (ttp80) cc_final: 0.4822 (tpt-90) REVERT: A 20 GLN cc_start: 0.6871 (tm-30) cc_final: 0.5542 (tp40) REVERT: A 21 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.5943 (mm) REVERT: B 20 GLN cc_start: 0.5691 (mm110) cc_final: 0.5190 (tp40) REVERT: B 209 ARG cc_start: 0.6843 (mtp-110) cc_final: 0.5391 (mmp80) REVERT: B 282 ARG cc_start: 0.7738 (mtp-110) cc_final: 0.6831 (mtt180) REVERT: B 385 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7477 (tt0) outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 0.6824 time to fit residues: 72.6509 Evaluate side-chains 95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.127932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100148 restraints weight = 6777.068| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.42 r_work: 0.3015 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6900 Z= 0.149 Angle : 0.531 5.450 9364 Z= 0.262 Chirality : 0.040 0.127 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.187 18.956 960 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.62 % Allowed : 15.49 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.27), residues: 896 helix: 2.09 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 64 TYR 0.008 0.001 TYR A 210 PHE 0.033 0.001 PHE B 357 TRP 0.003 0.001 TRP B 124 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6898) covalent geometry : angle 0.53091 / 0.26 ( 9360) SS BOND : bond 0.00682 / 0.35 ( 2) SS BOND : angle 1.27964 / 0.75 ( 4) hydrogen bonds : bond 0.03923 / 2.58 ( 508) hydrogen bonds : angle 4.01739 / 2.83 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6220 (ttp80) cc_final: 0.4820 (tpt-90) REVERT: A 20 GLN cc_start: 0.6911 (tm-30) cc_final: 0.5582 (tp40) REVERT: A 21 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5910 (mm) REVERT: B 20 GLN cc_start: 0.5699 (mm110) cc_final: 0.5172 (tp40) REVERT: B 209 ARG cc_start: 0.6814 (mtp-110) cc_final: 0.5360 (mmp80) REVERT: B 282 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.6825 (mtt180) REVERT: B 385 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7497 (tt0) outliers start: 11 outliers final: 5 residues processed: 97 average time/residue: 0.6782 time to fit residues: 68.7263 Evaluate side-chains 94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.128036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100419 restraints weight = 6688.573| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.40 r_work: 0.3018 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6900 Z= 0.150 Angle : 0.533 5.268 9364 Z= 0.263 Chirality : 0.040 0.127 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.180 18.645 960 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.18 % Allowed : 16.08 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.27), residues: 896 helix: 2.11 (0.19), residues: 686 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.008 0.001 TYR A 210 PHE 0.033 0.002 PHE B 357 TRP 0.003 0.001 TRP B 124 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 6898) covalent geometry : angle 0.53282 / 0.26 ( 9360) SS BOND : bond 0.00773 / 0.40 ( 2) SS BOND : angle 1.30754 / 0.76 ( 4) hydrogen bonds : bond 0.03927 / 2.59 ( 508) hydrogen bonds : angle 4.01758 / 2.83 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.6226 (ttp80) cc_final: 0.4841 (tpt-90) REVERT: A 20 GLN cc_start: 0.6927 (tm-30) cc_final: 0.5599 (tp40) REVERT: A 21 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5908 (mm) REVERT: A 167 ARG cc_start: 0.7003 (mpt180) cc_final: 0.6788 (mpt180) REVERT: B 20 GLN cc_start: 0.5722 (mm110) cc_final: 0.5190 (tp40) REVERT: B 209 ARG cc_start: 0.6720 (mtp-110) cc_final: 0.5331 (mmp80) REVERT: B 282 ARG cc_start: 0.7730 (mtp-110) cc_final: 0.6827 (mtt180) REVERT: B 385 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7401 (tt0) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 0.6947 time to fit residues: 70.3782 Evaluate side-chains 96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 385 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.127541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099844 restraints weight = 6734.035| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.42 r_work: 0.3011 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6900 Z= 0.159 Angle : 0.542 6.117 9364 Z= 0.267 Chirality : 0.041 0.128 1100 Planarity : 0.004 0.053 1176 Dihedral : 4.204 19.010 960 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.33 % Allowed : 16.22 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.27), residues: 896 helix: 2.08 (0.19), residues: 688 sheet: None (None), residues: 0 loop : -1.09 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 167 TYR 0.009 0.001 TYR A 210 PHE 0.033 0.002 PHE B 357 TRP 0.004 0.001 TRP B 124 HIS 0.002 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6898) covalent geometry : angle 0.54096 / 0.27 ( 9360) SS BOND : bond 0.00752 / 0.39 ( 2) SS BOND : angle 1.32822 / 0.78 ( 4) hydrogen bonds : bond 0.04002 / 2.64 ( 508) hydrogen bonds : angle 4.04563 / 2.85 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.84 seconds wall clock time: 41 minutes 12.50 seconds (2472.50 seconds total)