Starting phenix.real_space_refine on Thu Mar 6 09:29:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1i_37996/03_2025/8x1i_37996_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1i_37996/03_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_37996/03_2025/8x1i_37996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1i_37996/03_2025/8x1i_37996.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1i_37996/03_2025/8x1i_37996_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1i_37996/03_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-5624/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: 4.13, per 1000 atoms: 0.72 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: 1.60 Conformation dependent library (CDL) restraints added in 361.1 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: 0.66 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: 2.29 Time building geometry restraints manager: 1.92 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: 2.610 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.070 Process input model: 18.270 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:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- 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 : 0.481 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: 0.3915 time to fit residues: 33.5753 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 : 0.478 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075071 restraints weight = 24309.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078312 restraints weight = 10387.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080445 restraints weight = 5642.557| |-----------------------------------------------------------------------------| 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 : 0.459 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: 0.4858 time to fit residues: 29.3225 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 : 0.460 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079480 restraints weight = 25499.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082840 restraints weight = 10864.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085043 restraints weight = 6112.671| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2943 Z= 0.184 Angle : 0.675 7.558 3994 Z= 0.342 Chirality : 0.045 0.171 444 Planarity : 0.004 0.046 516 Dihedral : 11.464 92.050 412 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.61 % Allowed : 12.38 % 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: -0.95 (0.44), residues: 367 helix: 0.28 (0.50), residues: 119 sheet: -0.20 (0.63), residues: 70 loop : -1.43 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 277 HIS 0.002 0.001 HIS B 315 PHE 0.009 0.001 PHE B 328 TYR 0.008 0.001 TYR B 189 ARG 0.003 0.001 ARG B 269 *********************** 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 43 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.495 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 291 MET cc_start: 0.8976 (tpp) cc_final: 0.8658 (tpp) REVERT: B 323 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8288 (t) outliers start: 8 outliers final: 5 residues processed: 39 average time/residue: 0.3129 time to fit residues: 15.1518 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 : 0.487 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 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 279 ASN B 360 ASN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.092749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079543 restraints weight = 25573.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082879 restraints weight = 10796.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085043 restraints weight = 5953.243| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4953 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= 0.154 Angle : 0.627 7.057 3994 Z= 0.311 Chirality : 0.044 0.174 444 Planarity : 0.004 0.047 516 Dihedral : 9.940 78.957 410 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.61 % Allowed : 13.03 % 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: -0.70 (0.45), residues: 367 helix: 0.77 (0.53), residues: 113 sheet: -0.46 (0.61), residues: 69 loop : -1.25 (0.46), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 150 HIS 0.001 0.000 HIS B 315 PHE 0.007 0.001 PHE B 328 TYR 0.006 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 46 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.9104 (tpt) cc_final: 0.8895 (tpt) REVERT: B 291 MET cc_start: 0.8965 (tpp) cc_final: 0.8666 (tpp) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.3157 time to fit residues: 16.7401 Evaluate side-chains 37 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.092866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079527 restraints weight = 25147.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082807 restraints weight = 10568.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084947 restraints weight = 5915.064| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5326 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= 0.152 Angle : 0.608 6.512 3994 Z= 0.299 Chirality : 0.044 0.152 444 Planarity : 0.004 0.048 516 Dihedral : 9.188 68.999 409 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.28 % Allowed : 12.05 % Favored : 85.67 % 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: -0.54 (0.46), residues: 367 helix: 0.68 (0.52), residues: 122 sheet: -0.38 (0.59), residues: 74 loop : -1.05 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 95 HIS 0.001 0.000 HIS B 315 PHE 0.007 0.001 PHE B 159 TYR 0.005 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 39 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 MET cc_start: 0.9124 (tpt) cc_final: 0.8890 (tpt) REVERT: B 291 MET cc_start: 0.8943 (tpp) cc_final: 0.8661 (tpp) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.3079 time to fit residues: 13.3684 Evaluate side-chains 34 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.091210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077867 restraints weight = 25559.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081103 restraints weight = 10699.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083247 restraints weight = 6003.806| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5601 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= 0.203 Angle : 0.613 6.480 3994 Z= 0.302 Chirality : 0.044 0.152 444 Planarity : 0.004 0.046 516 Dihedral : 9.019 66.250 409 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.18 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: -0.58 (0.46), residues: 367 helix: 0.66 (0.51), residues: 122 sheet: -0.57 (0.56), residues: 80 loop : -1.01 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 150 HIS 0.002 0.001 HIS B 315 PHE 0.008 0.001 PHE B 328 TYR 0.010 0.002 TYR B 135 ARG 0.001 0.000 ARG B 155 *********************** 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 38 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.435 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 288 MET cc_start: 0.9180 (tpt) cc_final: 0.8862 (tpt) REVERT: B 291 MET cc_start: 0.8940 (tpp) cc_final: 0.8649 (tpp) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 0.2714 time to fit residues: 12.0766 Evaluate side-chains 33 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain B residue 357 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: 0.8980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.092769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079616 restraints weight = 25223.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082802 restraints weight = 10650.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.084931 restraints weight = 5921.003| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5785 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 : 0.591 5.963 3994 Z= 0.288 Chirality : 0.044 0.148 444 Planarity : 0.004 0.049 516 Dihedral : 8.368 61.666 407 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.28 % Allowed : 12.70 % 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: -0.33 (0.47), residues: 367 helix: 0.89 (0.52), residues: 122 sheet: -0.45 (0.56), residues: 80 loop : -0.87 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 95 HIS 0.002 0.000 HIS B 76 PHE 0.007 0.001 PHE B 78 TYR 0.007 0.001 TYR B 77 ARG 0.002 0.000 ARG B 172 *********************** 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 40 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.436 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 288 MET cc_start: 0.9130 (tpt) cc_final: 0.8824 (tpt) REVERT: B 291 MET cc_start: 0.8923 (tpp) cc_final: 0.8573 (tpp) outliers start: 7 outliers final: 4 residues processed: 37 average time/residue: 0.2783 time to fit residues: 13.0411 Evaluate side-chains 33 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 151 SER Chi-restraints excluded: chain B residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.092900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079413 restraints weight = 25061.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082705 restraints weight = 10671.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.084864 restraints weight = 6031.610| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5983 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= 0.144 Angle : 0.593 5.606 3994 Z= 0.287 Chirality : 0.044 0.149 444 Planarity : 0.004 0.049 516 Dihedral : 8.001 57.543 407 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.30 % Allowed : 13.03 % Favored : 85.67 % 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: 1.18 (0.54), residues: 116 sheet: -0.42 (0.56), residues: 79 loop : -0.84 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 95 HIS 0.004 0.001 HIS B 69 PHE 0.007 0.001 PHE B 78 TYR 0.016 0.001 TYR B 134 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 34 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.417 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: 0.5391 (t80) cc_final: 0.4863 (t80) REVERT: B 288 MET cc_start: 0.9187 (tpt) cc_final: 0.8825 (tpt) REVERT: B 291 MET cc_start: 0.8922 (tpp) cc_final: 0.8559 (tpp) outliers start: 4 outliers final: 3 residues processed: 32 average time/residue: 0.2807 time to fit residues: 11.3107 Evaluate side-chains 32 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.092656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079384 restraints weight = 25068.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082732 restraints weight = 10555.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084863 restraints weight = 5876.992| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6088 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= 0.147 Angle : 0.586 5.858 3994 Z= 0.282 Chirality : 0.044 0.149 444 Planarity : 0.004 0.046 516 Dihedral : 7.832 57.582 407 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.98 % Allowed : 13.36 % Favored : 85.67 % 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: 1.23 (0.53), residues: 116 sheet: -0.53 (0.56), residues: 80 loop : -0.80 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 95 HIS 0.001 0.000 HIS B 76 PHE 0.007 0.001 PHE B 78 TYR 0.006 0.001 TYR B 134 ARG 0.002 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 34 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 TYR cc_start: 0.5331 (t80) cc_final: 0.4803 (t80) REVERT: B 291 MET cc_start: 0.8935 (tpp) cc_final: 0.8567 (tpp) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.3042 time to fit residues: 13.1210 Evaluate side-chains 32 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.079306 restraints weight = 25421.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.082689 restraints weight = 10715.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084820 restraints weight = 5989.719| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6202 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= 0.148 Angle : 0.587 6.308 3994 Z= 0.283 Chirality : 0.044 0.138 444 Planarity : 0.004 0.047 516 Dihedral : 7.723 57.720 407 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.65 % Allowed : 13.68 % Favored : 85.67 % 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: -0.17 (0.47), residues: 367 helix: 1.21 (0.53), residues: 116 sheet: -0.40 (0.57), residues: 78 loop : -0.85 (0.51), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 95 HIS 0.003 0.001 HIS B 69 PHE 0.006 0.001 PHE B 328 TYR 0.011 0.001 TYR B 77 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 31 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 TYR cc_start: 0.5344 (t80) cc_final: 0.4811 (t80) REVERT: B 288 MET cc_start: 0.9239 (tpt) cc_final: 0.8799 (tpt) REVERT: B 291 MET cc_start: 0.8946 (tpp) cc_final: 0.8625 (tpp) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2810 time to fit residues: 10.9926 Evaluate side-chains 30 residues out of total 307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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: 4.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.092133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078704 restraints weight = 25505.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082073 restraints weight = 10718.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084178 restraints weight = 5978.010| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6308 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= 0.158 Angle : 0.596 6.478 3994 Z= 0.288 Chirality : 0.044 0.137 444 Planarity : 0.004 0.047 516 Dihedral : 7.681 58.169 407 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.65 % Allowed : 14.01 % 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: -0.31 (0.46), residues: 367 helix: 1.08 (0.52), residues: 122 sheet: -0.33 (0.57), residues: 78 loop : -1.08 (0.50), residues: 167 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 0.006 0.001 PHE B 217 TYR 0.012 0.001 TYR B 77 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: 3202.56 seconds wall clock time: 56 minutes 17.48 seconds (3377.48 seconds total)