Starting phenix.real_space_refine on Wed Feb 4 11:24:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950.map" model { file = "/net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0w_50950/02_2026/9g0w_50950_trim.cif" } resolution = 3.54 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 33 5.16 5 Cl 2 4.86 5 C 3402 2.51 5 N 781 2.21 5 O 842 1.98 5 H 5330 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10391 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5155 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 2 Chain: "A" Number of atoms: 5153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5153 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 2 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'CFA': 1, 'DLP': 1, 'DMS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.96, per 1000 atoms: 0.19 Number of scatterers: 10391 At special positions: 0 Unit cell: (62.759, 70.523, 108.049, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 33 16.00 P 1 15.00 O 842 8.00 N 781 7.00 C 3402 6.00 H 5330 1.00 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: 1.05 Conformation dependent library (CDL) restraints added in 434.6 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 3 through 30 removed outlier: 3.596A pdb=" N ILE B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 8 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Proline residue: B 16 - end of helix removed outlier: 3.592A pdb=" N SER B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.665A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 93 removed outlier: 3.780A pdb=" N PHE B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.897A pdb=" N TRP B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.697A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 4.099A pdb=" N ALA B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 removed outlier: 3.526A pdb=" N LEU B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.884A pdb=" N ILE B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.668A pdb=" N TYR B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.702A pdb=" N SER B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 282 through 294 removed outlier: 3.509A pdb=" N ILE B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.695A pdb=" N LYS B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 Processing helix chain 'B' and resid 327 through 336 removed outlier: 3.577A pdb=" N GLU B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 removed outlier: 3.977A pdb=" N THR B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU B 355 " --> pdb=" O MET B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'A' and resid 3 through 29 Proline residue: A 16 - end of helix removed outlier: 3.571A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 49 through 61 removed outlier: 3.563A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.783A pdb=" N MET A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 3.549A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.879A pdb=" N MET A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 removed outlier: 3.673A pdb=" N ILE A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 132 through 148 removed outlier: 4.372A pdb=" N SER A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.910A pdb=" N ILE A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 240 removed outlier: 3.648A pdb=" N TYR A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.839A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 274 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.617A pdb=" N MET A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.699A pdb=" N LEU A 323 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.560A pdb=" N MET A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 367 removed outlier: 3.605A pdb=" N ALA A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 1002 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: 2.43 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5324 1.03 - 1.23: 8 1.23 - 1.42: 2038 1.42 - 1.62: 3071 1.62 - 1.81: 62 Bond restraints: 10503 Sorted by residual: bond pdb=" C1' CFA A 401 " pdb=" O1' CFA A 401 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C2' CFA A 401 " pdb="CL3 CFA A 401 " ideal model delta sigma weight residual 1.727 1.785 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C4' CFA A 401 " pdb="CL4 CFA A 401 " ideal model delta sigma weight residual 1.733 1.784 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" O2P DLP A 403 " pdb=" P DLP A 403 " ideal model delta sigma weight residual 1.497 1.545 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" O1P DLP A 403 " pdb=" P DLP A 403 " ideal model delta sigma weight residual 1.502 1.544 -0.042 2.00e-02 2.50e+03 4.47e+00 ... (remaining 10498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.11: 19081 7.11 - 14.22: 13 14.22 - 21.32: 1 21.32 - 28.43: 0 28.43 - 35.54: 3 Bond angle restraints: 19098 Sorted by residual: angle pdb=" C LEU A 81 " pdb=" CA LEU A 81 " pdb=" HA LEU A 81 " ideal model delta sigma weight residual 109.00 73.46 35.54 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N LEU A 81 " pdb=" CA LEU A 81 " pdb=" HA LEU A 81 " ideal model delta sigma weight residual 110.00 75.52 34.48 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB LEU A 81 " pdb=" CA LEU A 81 " pdb=" HA LEU A 81 " ideal model delta sigma weight residual 109.00 77.41 31.59 3.00e+00 1.11e-01 1.11e+02 angle pdb=" O3P DLP A 403 " pdb=" P DLP A 403 " pdb=" O4P DLP A 403 " ideal model delta sigma weight residual 93.58 110.50 -16.92 3.00e+00 1.11e-01 3.18e+01 angle pdb=" N VAL B 316 " pdb=" CA VAL B 316 " pdb=" C VAL B 316 " ideal model delta sigma weight residual 112.96 108.70 4.26 1.00e+00 1.00e+00 1.81e+01 ... (remaining 19093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 4351 16.89 - 33.77: 381 33.77 - 50.66: 116 50.66 - 67.55: 43 67.55 - 84.44: 10 Dihedral angle restraints: 4901 sinusoidal: 2664 harmonic: 2237 Sorted by residual: dihedral pdb=" CA ILE A 353 " pdb=" C ILE A 353 " pdb=" N ALA A 354 " pdb=" CA ALA A 354 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" N LEU A 81 " pdb=" C LEU A 81 " pdb=" CA LEU A 81 " pdb=" CB LEU A 81 " ideal model delta harmonic sigma weight residual 122.80 132.28 -9.48 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C LEU A 81 " pdb=" N LEU A 81 " pdb=" CA LEU A 81 " pdb=" CB LEU A 81 " ideal model delta harmonic sigma weight residual -122.60 -132.05 9.45 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 4898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 820 0.084 - 0.167: 29 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA LEU A 81 " pdb=" N LEU A 81 " pdb=" C LEU A 81 " pdb=" CB LEU A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C2 DLP A 403 " pdb=" C1 DLP A 403 " pdb=" C3 DLP A 403 " pdb=" O2 DLP A 403 " both_signs ideal model delta sigma weight residual False -2.35 -2.59 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 848 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 355 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO B 356 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 356 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 356 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 22 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C THR B 22 " -0.020 2.00e-02 2.50e+03 pdb=" O THR B 22 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU B 23 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 35 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 36 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.015 5.00e-02 4.00e+02 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 651 2.21 - 2.81: 22081 2.81 - 3.40: 29107 3.40 - 4.00: 37464 4.00 - 4.60: 58753 Nonbonded interactions: 148056 Sorted by model distance: nonbonded pdb=" H LEU A 81 " pdb=" HA LEU A 81 " model vdw 1.609 1.816 nonbonded pdb=" O PHE A 293 " pdb=" HH TYR A 361 " model vdw 1.683 2.450 nonbonded pdb=" OE1 GLN B 57 " pdb=" HG SER B 256 " model vdw 1.731 2.450 nonbonded pdb=" HD1 HIS B 237 " pdb=" O TRP B 242 " model vdw 1.737 2.450 nonbonded pdb="HH21 ARG A 29 " pdb=" O ALA A 272 " model vdw 1.742 2.450 ... (remaining 148051 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 367) selection = (chain 'B' and (resid 2 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name H or name HA2)) or resid 105 through 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 238 through 367)) } 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 group one per residue 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: 6.980 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 0.067 5173 Z= 0.165 Angle : 0.760 16.919 7017 Z= 0.375 Chirality : 0.038 0.418 851 Planarity : 0.003 0.034 826 Dihedral : 13.939 84.200 1851 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.19 (0.37), residues: 628 helix: 1.33 (0.26), residues: 502 sheet: None (None), residues: 0 loop : -1.26 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.005 0.001 TYR B 336 PHE 0.009 0.001 PHE A 314 TRP 0.006 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5173) covalent geometry : angle 0.75958 ( 7017) hydrogen bonds : bond 0.13882 ( 340) hydrogen bonds : angle 5.69900 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9420 (mm) cc_final: 0.9146 (mm) REVERT: B 213 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8545 (ttmm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1422 time to fit residues: 26.9923 Evaluate side-chains 120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127379 restraints weight = 21689.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132145 restraints weight = 8878.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135187 restraints weight = 4629.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137070 restraints weight = 2787.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138245 restraints weight = 1834.190| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5173 Z= 0.156 Angle : 0.561 4.901 7017 Z= 0.286 Chirality : 0.038 0.401 851 Planarity : 0.004 0.031 826 Dihedral : 8.231 78.786 709 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 0.92 % Allowed : 8.61 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.37), residues: 628 helix: 1.31 (0.25), residues: 517 sheet: None (None), residues: 0 loop : -1.45 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.008 0.001 TYR A 130 PHE 0.012 0.001 PHE B 314 TRP 0.007 0.001 TRP B 233 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5173) covalent geometry : angle 0.56095 ( 7017) hydrogen bonds : bond 0.03546 ( 340) hydrogen bonds : angle 4.34900 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8613 (ttmm) REVERT: B 273 SER cc_start: 0.9098 (m) cc_final: 0.8695 (p) outliers start: 5 outliers final: 4 residues processed: 135 average time/residue: 0.1457 time to fit residues: 26.4492 Evaluate side-chains 127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 84 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126689 restraints weight = 22074.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131399 restraints weight = 9167.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134413 restraints weight = 4850.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136315 restraints weight = 2968.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137540 restraints weight = 1991.150| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5173 Z= 0.158 Angle : 0.551 5.925 7017 Z= 0.281 Chirality : 0.038 0.402 851 Planarity : 0.004 0.033 826 Dihedral : 7.897 80.047 709 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 0.92 % Allowed : 12.09 % Favored : 87.00 % 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: 1.24 (0.37), residues: 628 helix: 1.36 (0.25), residues: 516 sheet: None (None), residues: 0 loop : -1.64 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.008 0.001 TYR A 361 PHE 0.009 0.001 PHE A 238 TRP 0.014 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5173) covalent geometry : angle 0.55080 ( 7017) hydrogen bonds : bond 0.03393 ( 340) hydrogen bonds : angle 4.23720 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 SER cc_start: 0.9155 (m) cc_final: 0.8761 (p) REVERT: B 284 MET cc_start: 0.8330 (mmt) cc_final: 0.7762 (mmt) REVERT: A 63 ASN cc_start: 0.7734 (t0) cc_final: 0.6995 (t0) REVERT: A 289 MET cc_start: 0.7725 (mmp) cc_final: 0.6307 (ttt) outliers start: 5 outliers final: 4 residues processed: 127 average time/residue: 0.1516 time to fit residues: 25.3591 Evaluate side-chains 123 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125903 restraints weight = 21936.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130495 restraints weight = 9065.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133499 restraints weight = 4809.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135376 restraints weight = 2931.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136612 restraints weight = 1950.456| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5173 Z= 0.139 Angle : 0.538 5.286 7017 Z= 0.273 Chirality : 0.037 0.397 851 Planarity : 0.004 0.035 826 Dihedral : 7.936 82.409 709 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.10 % Allowed : 13.19 % Favored : 85.71 % 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: 1.31 (0.36), residues: 628 helix: 1.45 (0.25), residues: 517 sheet: None (None), residues: 0 loop : -1.86 (0.56), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.007 0.001 TYR A 361 PHE 0.013 0.001 PHE B 314 TRP 0.011 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5173) covalent geometry : angle 0.53835 ( 7017) hydrogen bonds : bond 0.03139 ( 340) hydrogen bonds : angle 4.06231 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9418 (mm) cc_final: 0.9179 (mm) REVERT: B 213 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8698 (ttmm) REVERT: B 273 SER cc_start: 0.9191 (m) cc_final: 0.8818 (p) REVERT: B 284 MET cc_start: 0.8363 (mmt) cc_final: 0.7854 (mmt) REVERT: A 30 HIS cc_start: 0.8107 (m-70) cc_final: 0.7598 (m90) REVERT: A 130 TYR cc_start: 0.7184 (m-80) cc_final: 0.6975 (m-80) REVERT: A 289 MET cc_start: 0.7765 (mmp) cc_final: 0.6406 (ttt) outliers start: 6 outliers final: 5 residues processed: 136 average time/residue: 0.1606 time to fit residues: 28.5666 Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 160 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124616 restraints weight = 21947.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129243 restraints weight = 9116.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132219 restraints weight = 4816.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134057 restraints weight = 2942.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135273 restraints weight = 1983.954| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5173 Z= 0.154 Angle : 0.545 4.917 7017 Z= 0.279 Chirality : 0.038 0.401 851 Planarity : 0.004 0.036 826 Dihedral : 7.945 83.965 709 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.47 % Allowed : 13.55 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.36), residues: 628 helix: 1.42 (0.25), residues: 517 sheet: None (None), residues: 0 loop : -1.98 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 216 TYR 0.008 0.001 TYR A 361 PHE 0.008 0.001 PHE B 330 TRP 0.012 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5173) covalent geometry : angle 0.54484 ( 7017) hydrogen bonds : bond 0.03256 ( 340) hydrogen bonds : angle 4.07714 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7809 (mttp) REVERT: B 137 ILE cc_start: 0.9442 (mm) cc_final: 0.9203 (mm) REVERT: B 213 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8692 (ttmm) REVERT: B 273 SER cc_start: 0.9186 (m) cc_final: 0.8821 (p) REVERT: B 284 MET cc_start: 0.8349 (mmt) cc_final: 0.7867 (mmt) REVERT: A 30 HIS cc_start: 0.8113 (m-70) cc_final: 0.7664 (m90) REVERT: A 130 TYR cc_start: 0.7219 (m-80) cc_final: 0.7000 (m-80) REVERT: A 160 ASN cc_start: 0.8383 (t0) cc_final: 0.8144 (p0) REVERT: A 212 LEU cc_start: 0.8162 (tp) cc_final: 0.7916 (mt) REVERT: A 289 MET cc_start: 0.7784 (mmp) cc_final: 0.6454 (ttt) outliers start: 8 outliers final: 7 residues processed: 130 average time/residue: 0.1623 time to fit residues: 27.8497 Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.1980 chunk 1 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126514 restraints weight = 21920.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131209 restraints weight = 9062.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134197 restraints weight = 4756.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136038 restraints weight = 2889.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137253 restraints weight = 1943.268| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5173 Z= 0.104 Angle : 0.515 5.178 7017 Z= 0.259 Chirality : 0.037 0.392 851 Planarity : 0.004 0.037 826 Dihedral : 7.682 84.230 709 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.10 % Allowed : 14.10 % Favored : 84.80 % 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: 1.49 (0.36), residues: 628 helix: 1.57 (0.25), residues: 518 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.005 0.001 TYR A 130 PHE 0.014 0.001 PHE B 314 TRP 0.010 0.001 TRP B 233 HIS 0.002 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5173) covalent geometry : angle 0.51541 ( 7017) hydrogen bonds : bond 0.02927 ( 340) hydrogen bonds : angle 3.90927 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7771 (mttp) REVERT: B 137 ILE cc_start: 0.9406 (mm) cc_final: 0.9177 (mm) REVERT: B 213 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8704 (ttmm) REVERT: B 273 SER cc_start: 0.9219 (m) cc_final: 0.8872 (p) REVERT: B 284 MET cc_start: 0.8263 (mmt) cc_final: 0.7803 (mmt) REVERT: A 30 HIS cc_start: 0.8121 (m-70) cc_final: 0.7635 (m90) REVERT: A 212 LEU cc_start: 0.8151 (tp) cc_final: 0.7918 (mt) REVERT: A 289 MET cc_start: 0.7749 (mmp) cc_final: 0.6383 (ttt) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.1610 time to fit residues: 27.9650 Evaluate side-chains 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.138680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124478 restraints weight = 21866.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129190 restraints weight = 9032.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132119 restraints weight = 4714.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134000 restraints weight = 2879.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.135266 restraints weight = 1913.892| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5173 Z= 0.155 Angle : 0.555 5.562 7017 Z= 0.283 Chirality : 0.038 0.399 851 Planarity : 0.004 0.036 826 Dihedral : 7.743 85.467 709 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.47 % Allowed : 14.84 % Favored : 83.70 % 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: 1.37 (0.36), residues: 628 helix: 1.52 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -2.06 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.011 0.001 TYR A 130 PHE 0.009 0.001 PHE B 330 TRP 0.014 0.001 TRP B 233 HIS 0.002 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5173) covalent geometry : angle 0.55460 ( 7017) hydrogen bonds : bond 0.03018 ( 340) hydrogen bonds : angle 3.94726 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7818 (mttp) REVERT: B 137 ILE cc_start: 0.9405 (mm) cc_final: 0.9177 (mm) REVERT: B 213 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8710 (ttmm) REVERT: B 273 SER cc_start: 0.9221 (m) cc_final: 0.8886 (p) REVERT: B 284 MET cc_start: 0.8281 (mmt) cc_final: 0.7861 (mmt) REVERT: B 345 THR cc_start: 0.8789 (p) cc_final: 0.8538 (t) REVERT: A 30 HIS cc_start: 0.8134 (m-70) cc_final: 0.7652 (m90) REVERT: A 212 LEU cc_start: 0.8193 (tp) cc_final: 0.7948 (mt) REVERT: A 246 GLU cc_start: 0.7404 (mp0) cc_final: 0.7160 (mp0) outliers start: 8 outliers final: 8 residues processed: 129 average time/residue: 0.1641 time to fit residues: 27.8321 Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 145 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.137563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123421 restraints weight = 21811.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128047 restraints weight = 9056.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130953 restraints weight = 4793.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132767 restraints weight = 2930.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133949 restraints weight = 1986.493| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5173 Z= 0.137 Angle : 0.550 6.342 7017 Z= 0.276 Chirality : 0.038 0.398 851 Planarity : 0.004 0.035 826 Dihedral : 7.782 86.738 709 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.47 % Allowed : 15.38 % Favored : 83.15 % 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: 1.39 (0.35), residues: 628 helix: 1.53 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -2.07 (0.55), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.008 0.001 TYR A 361 PHE 0.010 0.001 PHE A 293 TRP 0.014 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5173) covalent geometry : angle 0.54980 ( 7017) hydrogen bonds : bond 0.02941 ( 340) hydrogen bonds : angle 3.93296 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7809 (mttp) REVERT: B 137 ILE cc_start: 0.9410 (mm) cc_final: 0.9191 (mm) REVERT: B 213 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8711 (ttmm) REVERT: B 273 SER cc_start: 0.9208 (m) cc_final: 0.8897 (p) REVERT: B 284 MET cc_start: 0.8286 (mmt) cc_final: 0.7777 (mmt) REVERT: A 30 HIS cc_start: 0.8142 (m-70) cc_final: 0.7669 (m90) REVERT: A 130 TYR cc_start: 0.7866 (m-80) cc_final: 0.7527 (m-80) REVERT: A 212 LEU cc_start: 0.8200 (tp) cc_final: 0.7952 (mt) REVERT: A 289 MET cc_start: 0.7793 (mmm) cc_final: 0.6541 (ttp) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.1536 time to fit residues: 25.4971 Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 63 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124399 restraints weight = 21537.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129087 restraints weight = 8966.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131965 restraints weight = 4734.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133845 restraints weight = 2913.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135017 restraints weight = 1947.451| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5173 Z= 0.114 Angle : 0.542 6.573 7017 Z= 0.272 Chirality : 0.037 0.394 851 Planarity : 0.004 0.035 826 Dihedral : 7.687 86.424 709 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.47 % Allowed : 15.75 % Favored : 82.78 % 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: 1.62 (0.36), residues: 628 helix: 1.67 (0.24), residues: 517 sheet: None (None), residues: 0 loop : -1.79 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.008 0.001 TYR A 130 PHE 0.008 0.001 PHE B 330 TRP 0.013 0.001 TRP B 233 HIS 0.002 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5173) covalent geometry : angle 0.54228 ( 7017) hydrogen bonds : bond 0.02842 ( 340) hydrogen bonds : angle 3.82645 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7806 (mttm) REVERT: B 137 ILE cc_start: 0.9394 (mm) cc_final: 0.9179 (mm) REVERT: B 213 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8717 (ttmm) REVERT: B 273 SER cc_start: 0.9199 (m) cc_final: 0.8908 (p) REVERT: B 284 MET cc_start: 0.8265 (mmt) cc_final: 0.7710 (mmt) REVERT: B 345 THR cc_start: 0.8754 (p) cc_final: 0.8490 (t) REVERT: A 30 HIS cc_start: 0.8138 (m-70) cc_final: 0.7668 (m90) REVERT: A 130 TYR cc_start: 0.7996 (m-80) cc_final: 0.7741 (m-80) REVERT: A 212 LEU cc_start: 0.8196 (tp) cc_final: 0.7950 (mt) REVERT: A 246 GLU cc_start: 0.7567 (mp0) cc_final: 0.7267 (mp0) REVERT: A 289 MET cc_start: 0.7870 (mmm) cc_final: 0.6477 (ttp) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.1609 time to fit residues: 26.4784 Evaluate side-chains 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.122608 restraints weight = 21888.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127154 restraints weight = 9173.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130056 restraints weight = 4901.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131920 restraints weight = 3009.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133105 restraints weight = 2041.290| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5173 Z= 0.156 Angle : 0.563 6.880 7017 Z= 0.285 Chirality : 0.038 0.401 851 Planarity : 0.004 0.036 826 Dihedral : 7.813 87.975 709 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.47 % Allowed : 16.48 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.35), residues: 628 helix: 1.65 (0.24), residues: 517 sheet: None (None), residues: 0 loop : -1.87 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.010 0.001 TYR A 361 PHE 0.009 0.001 PHE B 330 TRP 0.014 0.001 TRP B 233 HIS 0.002 0.000 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5173) covalent geometry : angle 0.56251 ( 7017) hydrogen bonds : bond 0.02915 ( 340) hydrogen bonds : angle 3.89937 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7831 (mttp) REVERT: B 137 ILE cc_start: 0.9396 (mm) cc_final: 0.9180 (mm) REVERT: B 213 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8718 (ttmm) REVERT: B 273 SER cc_start: 0.9198 (m) cc_final: 0.8909 (p) REVERT: B 284 MET cc_start: 0.8317 (mmt) cc_final: 0.7821 (mmt) REVERT: A 30 HIS cc_start: 0.8154 (m-70) cc_final: 0.7683 (m90) REVERT: A 130 TYR cc_start: 0.8014 (m-80) cc_final: 0.7697 (m-80) REVERT: A 212 LEU cc_start: 0.8223 (tp) cc_final: 0.7973 (mt) REVERT: A 246 GLU cc_start: 0.7575 (mp0) cc_final: 0.7273 (mp0) REVERT: A 289 MET cc_start: 0.7868 (mmm) cc_final: 0.6511 (ttp) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.1584 time to fit residues: 26.3561 Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124808 restraints weight = 21826.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129436 restraints weight = 9024.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132366 restraints weight = 4775.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134222 restraints weight = 2911.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.135448 restraints weight = 1959.728| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5173 Z= 0.103 Angle : 0.535 7.125 7017 Z= 0.267 Chirality : 0.037 0.391 851 Planarity : 0.004 0.035 826 Dihedral : 7.696 87.780 709 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 17.22 % Favored : 81.50 % 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: 1.79 (0.36), residues: 628 helix: 1.80 (0.24), residues: 517 sheet: None (None), residues: 0 loop : -1.77 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 308 TYR 0.004 0.001 TYR A 361 PHE 0.008 0.001 PHE B 330 TRP 0.012 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5173) covalent geometry : angle 0.53483 ( 7017) hydrogen bonds : bond 0.02795 ( 340) hydrogen bonds : angle 3.77416 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.04 seconds wall clock time: 37 minutes 49.49 seconds (2269.49 seconds total)