Starting phenix.real_space_refine on Mon Jul 28 14:58:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g0w_50950/07_2025/9g0w_50950_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g0w_50950/07_2025/9g0w_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_50950/07_2025/9g0w_50950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g0w_50950/07_2025/9g0w_50950.map" model { file = "/net/cci-nas-00/data/ceres_data/9g0w_50950/07_2025/9g0w_50950_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g0w_50950/07_2025/9g0w_50950_trim.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.37, per 1000 atoms: 0.61 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: 2.92 Conformation dependent library (CDL) restraints added in 672.9 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: 0.81 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: 3.70 Time building geometry restraints manager: 3.47 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: 6.370 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: 0.190 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.720 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 233 HIS 0.001 0.000 HIS B 237 PHE 0.009 0.001 PHE A 314 TYR 0.005 0.001 TYR B 336 ARG 0.004 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.13882 ( 340) hydrogen bonds : angle 5.69900 ( 1002) covalent geometry : bond 0.00328 ( 5173) covalent geometry : angle 0.75958 ( 7017) *********************** 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 : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9420 (mm) cc_final: 0.9147 (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: 0.3199 time to fit residues: 60.1473 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 : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** 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 = 0.3599 r_free = 0.3599 target = 0.143350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128843 restraints weight = 21520.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133690 restraints weight = 8741.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136867 restraints weight = 4563.220| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5173 Z= 0.137 Angle : 0.548 4.742 7017 Z= 0.278 Chirality : 0.037 0.397 851 Planarity : 0.004 0.031 826 Dihedral : 8.214 78.670 709 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 0.73 % Allowed : 8.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.37), residues: 628 helix: 1.33 (0.25), residues: 518 sheet: None (None), residues: 0 loop : -1.41 (0.60), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 233 HIS 0.003 0.001 HIS B 253 PHE 0.010 0.001 PHE B 314 TYR 0.008 0.001 TYR A 130 ARG 0.002 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 340) hydrogen bonds : angle 4.34175 ( 1002) covalent geometry : bond 0.00313 ( 5173) covalent geometry : angle 0.54841 ( 7017) *********************** 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 133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8619 (ttmm) REVERT: B 273 SER cc_start: 0.9083 (m) cc_final: 0.8674 (p) outliers start: 4 outliers final: 4 residues processed: 132 average time/residue: 0.3293 time to fit residues: 57.7620 Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3529 r_free = 0.3529 target = 0.137636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123101 restraints weight = 22207.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127719 restraints weight = 9296.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130751 restraints weight = 4981.248| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5173 Z= 0.217 Angle : 0.588 5.924 7017 Z= 0.304 Chirality : 0.039 0.410 851 Planarity : 0.004 0.034 826 Dihedral : 8.040 80.720 709 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.66 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 11.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.36), residues: 628 helix: 1.25 (0.25), residues: 516 sheet: None (None), residues: 0 loop : -1.75 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 233 HIS 0.003 0.001 HIS A 237 PHE 0.010 0.001 PHE A 56 TYR 0.013 0.001 TYR A 361 ARG 0.002 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 340) hydrogen bonds : angle 4.32368 ( 1002) covalent geometry : bond 0.00496 ( 5173) covalent geometry : angle 0.58805 ( 7017) *********************** 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 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 273 SER cc_start: 0.9148 (m) cc_final: 0.8747 (p) REVERT: B 284 MET cc_start: 0.8373 (mmt) cc_final: 0.7776 (mmt) REVERT: A 30 HIS cc_start: 0.8143 (m-70) cc_final: 0.7657 (m90) REVERT: A 289 MET cc_start: 0.7794 (mmp) cc_final: 0.6411 (ttt) outliers start: 9 outliers final: 7 residues processed: 130 average time/residue: 0.3429 time to fit residues: 57.7922 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 : 0.751 ------------------------------------------------------------------------------- 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 84 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 345 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122039 restraints weight = 21793.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126635 restraints weight = 9026.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129631 restraints weight = 4814.517| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5173 Z= 0.146 Angle : 0.540 5.884 7017 Z= 0.274 Chirality : 0.038 0.397 851 Planarity : 0.004 0.035 826 Dihedral : 8.072 83.699 709 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 13.55 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.36), residues: 628 helix: 1.34 (0.25), residues: 517 sheet: None (None), residues: 0 loop : -1.91 (0.55), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 233 HIS 0.002 0.000 HIS B 237 PHE 0.011 0.001 PHE B 314 TYR 0.007 0.001 TYR A 361 ARG 0.002 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 340) hydrogen bonds : angle 4.10926 ( 1002) covalent geometry : bond 0.00336 ( 5173) covalent geometry : angle 0.53969 ( 7017) *********************** 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 136 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: B 66 LYS cc_start: 0.8063 (ttmm) cc_final: 0.7810 (mttp) REVERT: B 273 SER cc_start: 0.9159 (m) cc_final: 0.8776 (p) REVERT: B 284 MET cc_start: 0.8384 (mmt) cc_final: 0.7841 (mmt) REVERT: A 30 HIS cc_start: 0.8133 (m-70) cc_final: 0.7641 (m90) REVERT: A 130 TYR cc_start: 0.7213 (m-80) cc_final: 0.7002 (m-80) REVERT: A 212 LEU cc_start: 0.8189 (tp) cc_final: 0.7937 (mt) REVERT: A 289 MET cc_start: 0.7810 (mmp) cc_final: 0.6459 (ttt) outliers start: 6 outliers final: 5 residues processed: 133 average time/residue: 0.3275 time to fit residues: 57.5304 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 : 0.774 ------------------------------------------------------------------------------- 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 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.133958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120067 restraints weight = 21972.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124351 restraints weight = 9517.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.127221 restraints weight = 5197.477| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5173 Z= 0.125 Angle : 0.531 6.015 7017 Z= 0.269 Chirality : 0.037 0.397 851 Planarity : 0.004 0.036 826 Dihedral : 7.826 84.026 709 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 13.00 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.36), residues: 628 helix: 1.43 (0.25), residues: 518 sheet: None (None), residues: 0 loop : -1.87 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 233 HIS 0.002 0.000 HIS B 237 PHE 0.008 0.001 PHE B 330 TYR 0.006 0.001 TYR A 361 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 340) hydrogen bonds : angle 3.98896 ( 1002) covalent geometry : bond 0.00294 ( 5173) covalent geometry : angle 0.53134 ( 7017) *********************** 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: 6 poor density : 129 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9474 (mm) cc_final: 0.9244 (mm) REVERT: B 273 SER cc_start: 0.9142 (m) cc_final: 0.8783 (p) REVERT: B 284 MET cc_start: 0.8342 (mmt) cc_final: 0.7888 (mmt) REVERT: A 30 HIS cc_start: 0.8071 (m-70) cc_final: 0.7630 (m90) REVERT: A 130 TYR cc_start: 0.7191 (m-80) cc_final: 0.6977 (m-80) REVERT: A 212 LEU cc_start: 0.8161 (tp) cc_final: 0.7933 (mt) REVERT: A 289 MET cc_start: 0.7758 (mmp) cc_final: 0.6558 (ttt) outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.3523 time to fit residues: 61.9507 Evaluate side-chains 128 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.130941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116686 restraints weight = 22192.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.121114 restraints weight = 9414.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123964 restraints weight = 5083.123| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5173 Z= 0.134 Angle : 0.530 6.307 7017 Z= 0.269 Chirality : 0.037 0.399 851 Planarity : 0.004 0.036 826 Dihedral : 7.782 85.237 709 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.47 % Allowed : 14.29 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.36), residues: 628 helix: 1.46 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.014 0.001 PHE B 314 TYR 0.007 0.001 TYR A 361 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 340) hydrogen bonds : angle 3.93802 ( 1002) covalent geometry : bond 0.00312 ( 5173) covalent geometry : angle 0.53019 ( 7017) *********************** 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 133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.820 Fit side-chains REVERT: B 137 ILE cc_start: 0.9481 (mm) cc_final: 0.9250 (mm) REVERT: B 273 SER cc_start: 0.9117 (m) cc_final: 0.8782 (p) REVERT: B 284 MET cc_start: 0.8316 (mmt) cc_final: 0.7888 (mmt) REVERT: A 30 HIS cc_start: 0.8036 (m-70) cc_final: 0.7627 (m90) REVERT: A 130 TYR cc_start: 0.7200 (m-80) cc_final: 0.6985 (m-80) REVERT: A 212 LEU cc_start: 0.8174 (tp) cc_final: 0.7948 (mt) REVERT: A 289 MET cc_start: 0.7765 (mmp) cc_final: 0.6620 (ttt) outliers start: 8 outliers final: 6 residues processed: 130 average time/residue: 0.3216 time to fit residues: 55.8896 Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN A 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123994 restraints weight = 22236.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128539 restraints weight = 9150.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131392 restraints weight = 4780.844| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5173 Z= 0.130 Angle : 0.539 6.337 7017 Z= 0.273 Chirality : 0.037 0.398 851 Planarity : 0.004 0.036 826 Dihedral : 7.767 85.833 709 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.36), residues: 628 helix: 1.53 (0.24), residues: 518 sheet: None (None), residues: 0 loop : -1.98 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.011 0.001 PHE B 314 TYR 0.007 0.001 TYR A 361 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 340) hydrogen bonds : angle 3.91262 ( 1002) covalent geometry : bond 0.00305 ( 5173) covalent geometry : angle 0.53932 ( 7017) *********************** 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 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9464 (mm) cc_final: 0.9237 (mm) REVERT: B 273 SER cc_start: 0.9150 (m) cc_final: 0.8825 (p) REVERT: B 284 MET cc_start: 0.8302 (mmt) cc_final: 0.7868 (mmt) REVERT: B 345 THR cc_start: 0.8741 (p) cc_final: 0.8484 (t) REVERT: A 30 HIS cc_start: 0.8079 (m-70) cc_final: 0.7656 (m90) REVERT: A 130 TYR cc_start: 0.7242 (m-80) cc_final: 0.7031 (m-80) REVERT: A 212 LEU cc_start: 0.8190 (tp) cc_final: 0.7959 (mt) REVERT: A 246 GLU cc_start: 0.7324 (mp0) cc_final: 0.7061 (mp0) REVERT: A 289 MET cc_start: 0.7776 (mmp) cc_final: 0.6531 (ttt) outliers start: 7 outliers final: 6 residues processed: 127 average time/residue: 0.3242 time to fit residues: 54.9258 Evaluate side-chains 123 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3523 r_free = 0.3523 target = 0.137471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123954 restraints weight = 21967.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128439 restraints weight = 9099.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131256 restraints weight = 4781.935| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5173 Z= 0.128 Angle : 0.543 6.786 7017 Z= 0.272 Chirality : 0.037 0.396 851 Planarity : 0.004 0.036 826 Dihedral : 7.762 86.454 709 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 1.28 % Allowed : 16.30 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.36), residues: 628 helix: 1.60 (0.24), residues: 519 sheet: None (None), residues: 0 loop : -1.98 (0.55), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.011 0.001 PHE B 314 TYR 0.007 0.001 TYR A 361 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02898 ( 340) hydrogen bonds : angle 3.86999 ( 1002) covalent geometry : bond 0.00303 ( 5173) covalent geometry : angle 0.54333 ( 7017) *********************** 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 127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9458 (mm) cc_final: 0.9234 (mm) REVERT: B 273 SER cc_start: 0.9160 (m) cc_final: 0.8835 (p) REVERT: B 284 MET cc_start: 0.8301 (mmt) cc_final: 0.7872 (mmt) REVERT: A 30 HIS cc_start: 0.8097 (m-70) cc_final: 0.7672 (m90) REVERT: A 212 LEU cc_start: 0.8205 (tp) cc_final: 0.7962 (mt) REVERT: A 289 MET cc_start: 0.7786 (mmp) cc_final: 0.6479 (ttt) outliers start: 7 outliers final: 6 residues processed: 124 average time/residue: 0.3179 time to fit residues: 52.6595 Evaluate side-chains 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3520 r_free = 0.3520 target = 0.137156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123517 restraints weight = 22127.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128040 restraints weight = 9158.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130863 restraints weight = 4803.660| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5173 Z= 0.131 Angle : 0.543 6.587 7017 Z= 0.274 Chirality : 0.037 0.397 851 Planarity : 0.004 0.036 826 Dihedral : 7.778 87.145 709 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.35), residues: 628 helix: 1.64 (0.24), residues: 516 sheet: None (None), residues: 0 loop : -1.79 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.010 0.001 PHE B 314 TYR 0.011 0.001 TYR A 130 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 340) hydrogen bonds : angle 3.85648 ( 1002) covalent geometry : bond 0.00307 ( 5173) covalent geometry : angle 0.54310 ( 7017) *********************** 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 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9453 (mm) cc_final: 0.9231 (mm) REVERT: B 273 SER cc_start: 0.9121 (m) cc_final: 0.8819 (p) REVERT: B 284 MET cc_start: 0.8303 (mmt) cc_final: 0.7929 (mmt) REVERT: B 345 THR cc_start: 0.8743 (p) cc_final: 0.8476 (t) REVERT: A 30 HIS cc_start: 0.8091 (m-70) cc_final: 0.7674 (m90) REVERT: A 212 LEU cc_start: 0.8207 (tp) cc_final: 0.7971 (mt) REVERT: A 246 GLU cc_start: 0.7509 (mp0) cc_final: 0.7193 (mp0) outliers start: 6 outliers final: 6 residues processed: 124 average time/residue: 0.3534 time to fit residues: 59.3028 Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.137227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123645 restraints weight = 21882.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128140 restraints weight = 9042.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130896 restraints weight = 4759.206| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5173 Z= 0.130 Angle : 0.556 7.172 7017 Z= 0.277 Chirality : 0.038 0.397 851 Planarity : 0.004 0.036 826 Dihedral : 7.786 87.520 709 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.28 % Allowed : 17.03 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.36), residues: 628 helix: 1.64 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.82 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.010 0.001 PHE B 314 TYR 0.007 0.001 TYR A 361 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 340) hydrogen bonds : angle 3.85704 ( 1002) covalent geometry : bond 0.00305 ( 5173) covalent geometry : angle 0.55564 ( 7017) ********************** 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 127 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ILE cc_start: 0.9451 (mm) cc_final: 0.9232 (mm) REVERT: B 273 SER cc_start: 0.9107 (m) cc_final: 0.8817 (p) REVERT: B 284 MET cc_start: 0.8296 (mmt) cc_final: 0.7857 (mmt) REVERT: B 345 THR cc_start: 0.8763 (p) cc_final: 0.8495 (t) REVERT: A 30 HIS cc_start: 0.8092 (m-70) cc_final: 0.7666 (m90) REVERT: A 130 TYR cc_start: 0.7933 (m-80) cc_final: 0.7679 (m-80) REVERT: A 212 LEU cc_start: 0.8213 (tp) cc_final: 0.7975 (mt) REVERT: A 246 GLU cc_start: 0.7504 (mp0) cc_final: 0.7202 (mp0) REVERT: A 289 MET cc_start: 0.7745 (mmm) cc_final: 0.6562 (ttt) outliers start: 7 outliers final: 6 residues processed: 125 average time/residue: 0.3369 time to fit residues: 56.7661 Evaluate side-chains 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3528 r_free = 0.3528 target = 0.137236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122964 restraints weight = 21884.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127616 restraints weight = 9090.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130490 restraints weight = 4788.238| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5173 Z= 0.131 Angle : 0.554 6.948 7017 Z= 0.279 Chirality : 0.038 0.397 851 Planarity : 0.004 0.036 826 Dihedral : 7.787 87.968 709 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.82 % Rotamer: Outliers : 1.28 % Allowed : 17.40 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.36), residues: 628 helix: 1.68 (0.24), residues: 520 sheet: None (None), residues: 0 loop : -1.82 (0.57), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 233 HIS 0.003 0.000 HIS A 237 PHE 0.010 0.001 PHE B 314 TYR 0.011 0.001 TYR A 130 ARG 0.001 0.000 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 340) hydrogen bonds : angle 3.83586 ( 1002) covalent geometry : bond 0.00309 ( 5173) covalent geometry : angle 0.55375 ( 7017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4111.71 seconds wall clock time: 70 minutes 50.88 seconds (4250.88 seconds total)