Starting phenix.real_space_refine on Tue Jan 14 05:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1i_37996/01_2025/8x1i_37996_trim.cif" } resolution = 4.0 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= 0.006 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 2 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 1829 2.51 5 N 484 2.21 5 O 553 1.98 5 H 2840 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5722 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5694 Classifications: {'peptide': 369} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 350} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.88, per 1000 atoms: 0.68 Number of scatterers: 5722 At special positions: 0 Unit cell: (80.3, 55, 80.3, 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) S 13 16.00 P 2 15.00 Mg 1 11.99 O 553 8.00 N 484 7.00 C 1829 6.00 H 2840 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: 1.63 Conformation dependent library (CDL) restraints added in 480.0 milliseconds 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 43.9% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 44 through 48 removed outlier: 4.161A pdb=" N GLY B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.839A pdb=" N GLU B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.520A pdb=" N THR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.525A pdb=" N TYR B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.652A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 234 through 249 removed outlier: 3.760A pdb=" N ALA B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.926A pdb=" N LEU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 removed outlier: 4.138A pdb=" N SER B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 312 removed outlier: 5.305A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 320 through 328 removed outlier: 3.998A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 359 through 364 removed outlier: 4.110A pdb=" N LYS B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 30 removed outlier: 6.226A pdb=" N LEU B 7 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY B 127 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 9 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA B 122 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 169 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE B 124 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER B 171 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 126 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL B 173 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR B 128 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 62 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AA3, first strand: chain 'B' and resid 221 through 222 removed outlier: 7.506A pdb=" N TYR B 201 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 318 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 203 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 277 122 hydrogen bonds defined for protein. 321 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: 2.18 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2838 1.13 - 1.30: 511 1.30 - 1.47: 1102 1.47 - 1.65: 1308 1.65 - 1.82: 24 Bond restraints: 5783 Sorted by residual: bond pdb=" N ILE B 352 " pdb=" H ILE B 352 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 TYR B 93 " pdb=" HD2 TYR B 93 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLU B 90 " pdb=" H GLU B 90 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N THR B 128 " pdb=" H THR B 128 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ALA B 137 " pdb=" H ALA B 137 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 5778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 9906 4.38 - 8.76: 555 8.76 - 13.14: 11 13.14 - 17.52: 0 17.52 - 21.90: 1 Bond angle restraints: 10473 Sorted by residual: angle pdb=" N PRO B 225 " pdb=" CA PRO B 225 " pdb=" C PRO B 225 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.08e+01 angle pdb=" O1B ADP B 401 " pdb=" PB ADP B 401 " pdb=" O2B ADP B 401 " ideal model delta sigma weight residual 119.90 98.00 21.90 3.00e+00 1.11e-01 5.33e+01 angle pdb=" CB HIS B 253 " pdb=" CG HIS B 253 " pdb=" CD2 HIS B 253 " ideal model delta sigma weight residual 131.20 124.62 6.58 1.30e+00 5.92e-01 2.56e+01 angle pdb=" C ASN B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 119.05 124.59 -5.54 1.11e+00 8.12e-01 2.49e+01 angle pdb=" C ILE B 168 " pdb=" N ILE B 169 " pdb=" CA ILE B 169 " ideal model delta sigma weight residual 120.70 126.81 -6.11 1.25e+00 6.40e-01 2.39e+01 ... (remaining 10468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.15: 2544 27.15 - 54.31: 116 54.31 - 81.46: 55 81.46 - 108.61: 1 108.61 - 135.77: 2 Dihedral angle restraints: 2718 sinusoidal: 1491 harmonic: 1227 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.77 -135.77 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.84 135.16 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" CA ASP B 12 " pdb=" C ASP B 12 " pdb=" N PRO B 13 " pdb=" CA PRO B 13 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 2715 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.091: 292 0.091 - 0.182: 121 0.182 - 0.273: 26 0.273 - 0.364: 4 0.364 - 0.454: 1 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA PRO B 225 " pdb=" N PRO B 225 " pdb=" C PRO B 225 " pdb=" CB PRO B 225 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA LEU B 357 " pdb=" N LEU B 357 " pdb=" C LEU B 357 " pdb=" CB LEU B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA ASP B 12 " pdb=" N ASP B 12 " pdb=" C ASP B 12 " pdb=" CB ASP B 12 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 441 not shown) Planarity restraints: 866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 401 " -0.313 2.00e-02 2.50e+03 1.27e-01 4.44e+02 pdb=" C2 ADP B 401 " 0.058 2.00e-02 2.50e+03 pdb=" C4 ADP B 401 " 0.085 2.00e-02 2.50e+03 pdb=" C5 ADP B 401 " 0.034 2.00e-02 2.50e+03 pdb=" C6 ADP B 401 " -0.048 2.00e-02 2.50e+03 pdb=" C8 ADP B 401 " 0.115 2.00e-02 2.50e+03 pdb=" N1 ADP B 401 " -0.031 2.00e-02 2.50e+03 pdb=" N3 ADP B 401 " 0.103 2.00e-02 2.50e+03 pdb=" N6 ADP B 401 " -0.165 2.00e-02 2.50e+03 pdb=" N7 ADP B 401 " 0.064 2.00e-02 2.50e+03 pdb=" N9 ADP B 401 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 95 " -0.198 2.00e-02 2.50e+03 7.98e-02 2.55e+02 pdb=" CG TRP B 95 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 95 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 95 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP B 95 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 TRP B 95 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP B 95 " 0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 95 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 95 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP B 95 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP B 95 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP B 95 " 0.107 2.00e-02 2.50e+03 pdb=" HE3 TRP B 95 " 0.109 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 95 " -0.082 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 95 " 0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP B 95 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 210 " -0.293 9.50e-02 1.11e+02 1.38e-01 2.26e+02 pdb=" NE ARG B 210 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 210 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG B 210 " -0.106 2.00e-02 2.50e+03 pdb=" NH2 ARG B 210 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 210 " 0.207 2.00e-02 2.50e+03 pdb="HH12 ARG B 210 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG B 210 " 0.141 2.00e-02 2.50e+03 pdb="HH22 ARG B 210 " -0.024 2.00e-02 2.50e+03 ... (remaining 863 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 467 2.22 - 2.81: 10970 2.81 - 3.41: 16009 3.41 - 4.00: 20764 4.00 - 4.60: 30904 Nonbonded interactions: 79114 Sorted by model distance: nonbonded pdb=" HG SER B 81 " pdb=" OE2 GLU B 84 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASP B 98 " pdb=" HG SER B 100 " model vdw 1.635 2.450 nonbonded pdb=" OD1 ASP B 213 " pdb=" HG SER B 230 " model vdw 1.637 2.450 nonbonded pdb=" HG1 THR B 25 " pdb=" OE2 GLU B 56 " model vdw 1.638 2.450 nonbonded pdb=" OE1 GLU B 263 " pdb=" HH TYR B 275 " model vdw 1.644 2.450 ... (remaining 79109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.012 0.142 2943 Z= 0.813 Angle : 1.871 21.904 3994 Z= 1.188 Chirality : 0.102 0.454 444 Planarity : 0.014 0.127 516 Dihedral : 15.720 135.766 1083 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.93 % Allowed : 4.56 % Favored : 92.51 % Cbeta Deviations : 0.30 % 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: -2.05 (0.39), residues: 367 helix: -1.86 (0.40), residues: 106 sheet: -0.06 (0.63), residues: 60 loop : -1.46 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.125 0.029 TRP B 95 HIS 0.011 0.004 HIS B 69 PHE 0.080 0.015 PHE B 268 TYR 0.102 0.018 TYR B 275 ARG 0.007 0.001 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.4243 time to fit residues: 36.2279 Evaluate side-chains 56 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075072 restraints weight = 24309.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078307 restraints weight = 10364.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080440 restraints weight = 5651.902| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2943 Z= 0.218 Angle : 0.774 7.296 3994 Z= 0.406 Chirality : 0.048 0.171 444 Planarity : 0.005 0.047 516 Dihedral : 13.124 107.884 414 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.61 % Allowed : 9.77 % Favored : 87.62 % 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: -1.54 (0.41), residues: 367 helix: -0.42 (0.47), residues: 119 sheet: -0.28 (0.59), residues: 70 loop : -1.73 (0.42), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 277 HIS 0.002 0.001 HIS B 315 PHE 0.014 0.002 PHE B 328 TYR 0.013 0.002 TYR B 189 ARG 0.006 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 323 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8099 (t) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.4709 time to fit residues: 28.5375 Evaluate side-chains 38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.0270 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.093570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080285 restraints weight = 25401.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083567 restraints weight = 10967.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.085792 restraints weight = 6117.655| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2943 Z= 0.164 Angle : 0.673 7.373 3994 Z= 0.340 Chirality : 0.045 0.175 444 Planarity : 0.004 0.046 516 Dihedral : 11.479 93.050 412 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.93 % Allowed : 12.70 % Favored : 84.36 % 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: -0.81 (0.44), residues: 367 helix: 0.49 (0.51), residues: 113 sheet: -0.16 (0.63), residues: 70 loop : -1.34 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 277 HIS 0.001 0.000 HIS B 315 PHE 0.009 0.001 PHE B 159 TYR 0.007 0.001 TYR B 189 ARG 0.003 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 TYR cc_start: 0.8558 (t80) cc_final: 0.8288 (t80) REVERT: B 291 MET cc_start: 0.8964 (tpp) cc_final: 0.8665 (tpp) REVERT: B 323 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8349 (t) outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.3136 time to fit residues: 16.5372 Evaluate side-chains 40 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.092978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079520 restraints weight = 25531.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082885 restraints weight = 10861.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.085080 restraints weight = 6005.705| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2943 Z= 0.157 Angle : 0.631 7.193 3994 Z= 0.313 Chirality : 0.045 0.168 444 Planarity : 0.004 0.046 516 Dihedral : 10.079 81.495 410 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.28 % Allowed : 13.68 % Favored : 84.04 % 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: -0.70 (0.45), residues: 367 helix: 0.76 (0.52), residues: 113 sheet: -0.42 (0.61), residues: 70 loop : -1.26 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 277 HIS 0.001 0.000 HIS B 315 PHE 0.007 0.001 PHE B 159 TYR 0.008 0.001 TYR B 125 ARG 0.002 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.8969 (tpp) cc_final: 0.8651 (tpp) REVERT: B 323 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (t) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.2895 time to fit residues: 14.4128 Evaluate side-chains 37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079385 restraints weight = 25132.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082728 restraints weight = 10505.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084880 restraints weight = 5805.581| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2943 Z= 0.173 Angle : 0.622 6.775 3994 Z= 0.307 Chirality : 0.044 0.152 444 Planarity : 0.004 0.047 516 Dihedral : 9.513 71.624 410 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.63 % Allowed : 13.36 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.63 (0.46), residues: 367 helix: 0.54 (0.51), residues: 121 sheet: -0.19 (0.62), residues: 70 loop : -1.18 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 95 HIS 0.001 0.000 HIS B 315 PHE 0.007 0.001 PHE B 159 TYR 0.006 0.001 TYR B 125 ARG 0.001 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.3215 time to fit residues: 14.8198 Evaluate side-chains 38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.078366 restraints weight = 25430.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081633 restraints weight = 10736.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083760 restraints weight = 5952.763| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2943 Z= 0.191 Angle : 0.620 6.376 3994 Z= 0.304 Chirality : 0.044 0.148 444 Planarity : 0.004 0.047 516 Dihedral : 9.109 66.867 409 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.34 % 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: -0.63 (0.46), residues: 367 helix: 0.55 (0.51), residues: 123 sheet: -0.40 (0.59), residues: 74 loop : -1.09 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 95 HIS 0.002 0.001 HIS B 69 PHE 0.018 0.001 PHE B 268 TYR 0.008 0.001 TYR B 135 ARG 0.001 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8545 (t) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.2764 time to fit residues: 13.3558 Evaluate side-chains 35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076923 restraints weight = 25666.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080069 restraints weight = 11416.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082074 restraints weight = 6546.350| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2943 Z= 0.265 Angle : 0.654 6.699 3994 Z= 0.324 Chirality : 0.045 0.144 444 Planarity : 0.004 0.047 516 Dihedral : 9.036 72.525 409 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.95 % Allowed : 13.36 % Favored : 84.69 % 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: -0.78 (0.45), residues: 367 helix: 0.35 (0.50), residues: 124 sheet: -0.61 (0.57), residues: 75 loop : -1.06 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 150 HIS 0.003 0.001 HIS B 315 PHE 0.011 0.001 PHE B 268 TYR 0.015 0.002 TYR B 135 ARG 0.002 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8645 (t) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.2931 time to fit residues: 12.8253 Evaluate side-chains 37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078169 restraints weight = 24948.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081510 restraints weight = 10582.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083709 restraints weight = 5904.008| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2943 Z= 0.147 Angle : 0.602 5.917 3994 Z= 0.290 Chirality : 0.043 0.147 444 Planarity : 0.004 0.049 516 Dihedral : 8.337 63.241 407 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.63 % Allowed : 13.03 % Favored : 85.34 % 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: -0.43 (0.46), residues: 367 helix: 0.77 (0.52), residues: 122 sheet: -0.58 (0.56), residues: 75 loop : -0.85 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 237 HIS 0.001 0.000 HIS B 76 PHE 0.013 0.001 PHE B 268 TYR 0.007 0.001 TYR B 77 ARG 0.001 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 323 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8561 (t) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.2812 time to fit residues: 12.8171 Evaluate side-chains 37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077623 restraints weight = 25154.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.080973 restraints weight = 10806.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.083141 restraints weight = 6075.694| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2943 Z= 0.169 Angle : 0.607 6.052 3994 Z= 0.293 Chirality : 0.044 0.144 444 Planarity : 0.004 0.048 516 Dihedral : 8.123 59.009 407 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.95 % Allowed : 13.36 % Favored : 84.69 % 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: -0.39 (0.47), residues: 367 helix: 0.80 (0.52), residues: 123 sheet: -0.41 (0.56), residues: 79 loop : -0.93 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 95 HIS 0.001 0.000 HIS B 76 PHE 0.011 0.001 PHE B 268 TYR 0.015 0.002 TYR B 134 ARG 0.001 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.8980 (tpp) cc_final: 0.8597 (tpp) REVERT: B 323 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8555 (t) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 0.2848 time to fit residues: 12.6634 Evaluate side-chains 37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.078664 restraints weight = 25247.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082054 restraints weight = 10835.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084259 restraints weight = 6054.957| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2943 Z= 0.142 Angle : 0.594 6.235 3994 Z= 0.284 Chirality : 0.043 0.143 444 Planarity : 0.004 0.047 516 Dihedral : 7.780 57.408 407 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.30 % Allowed : 14.01 % Favored : 84.69 % 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: -0.19 (0.47), residues: 367 helix: 1.25 (0.54), residues: 117 sheet: -0.36 (0.57), residues: 79 loop : -0.96 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 150 HIS 0.001 0.000 HIS B 76 PHE 0.010 0.001 PHE B 268 TYR 0.013 0.001 TYR B 134 ARG 0.001 0.000 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 TYR cc_start: 0.5341 (t80) cc_final: 0.4828 (t80) REVERT: B 291 MET cc_start: 0.8955 (tpp) cc_final: 0.8592 (tpp) REVERT: B 298 ASP cc_start: 0.7682 (m-30) cc_final: 0.7201 (m-30) REVERT: B 323 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8506 (t) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.2774 time to fit residues: 13.7945 Evaluate side-chains 35 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078113 restraints weight = 25310.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081451 restraints weight = 10838.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083625 restraints weight = 6085.344| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2943 Z= 0.149 Angle : 0.591 6.743 3994 Z= 0.283 Chirality : 0.043 0.141 444 Planarity : 0.004 0.048 516 Dihedral : 7.709 57.963 407 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.98 % Allowed : 14.66 % Favored : 84.36 % 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: -0.18 (0.47), residues: 367 helix: 1.13 (0.53), residues: 123 sheet: -0.17 (0.59), residues: 76 loop : -1.00 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 95 HIS 0.001 0.000 HIS B 76 PHE 0.007 0.001 PHE B 268 TYR 0.011 0.001 TYR B 134 ARG 0.002 0.000 ARG B 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.91 seconds wall clock time: 48 minutes 50.52 seconds (2930.52 seconds total)