Starting phenix.real_space_refine on Thu Mar 6 09:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb7_19027/03_2025/8rb7_19027.cif" } resolution = 3.2 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 1840 2.51 5 N 508 2.21 5 O 538 1.98 5 H 2948 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 5848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Chain: "B" Number of atoms: 2924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2924 Classifications: {'peptide': 180} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 3.30, per 1000 atoms: 0.56 Number of scatterers: 5848 At special positions: 0 Unit cell: (73.216, 134.784, 50.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 538 8.00 N 508 7.00 C 1840 6.00 H 2948 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: 1.35 Conformation dependent library (CDL) restraints added in 368.9 milliseconds 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 688 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 73.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 198 through 208 removed outlier: 3.553A pdb=" N ARG A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 264 through 282 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 305 through 319 removed outlier: 4.203A pdb=" N GLY A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.625A pdb=" N TRP B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.599A pdb=" N ASN B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.808A pdb=" N LEU B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 305 through 319 Processing helix chain 'B' and resid 323 through 336 177 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 818 1.09 - 1.27: 2629 1.27 - 1.45: 737 1.45 - 1.63: 1696 1.63 - 1.82: 22 Bond restraints: 5902 Sorted by residual: bond pdb=" N THR A 189 " pdb=" H THR A 189 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N LYS A 164 " pdb=" H LYS A 164 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NH1 ARG A 166 " pdb="HH12 ARG A 166 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NH1 ARG A 278 " pdb="HH12 ARG A 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 PHE A 168 " pdb=" HE1 PHE A 168 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 5897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 8860 2.47 - 4.94: 1406 4.94 - 7.40: 387 7.40 - 9.87: 63 9.87 - 12.34: 6 Bond angle restraints: 10722 Sorted by residual: angle pdb=" C ASP A 317 " pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 120.38 127.94 -7.56 1.37e+00 5.33e-01 3.05e+01 angle pdb=" C ASP B 317 " pdb=" N GLN B 318 " pdb=" CA GLN B 318 " ideal model delta sigma weight residual 120.28 127.60 -7.32 1.34e+00 5.57e-01 2.98e+01 angle pdb=" C SER B 250 " pdb=" N GLN B 251 " pdb=" CA GLN B 251 " ideal model delta sigma weight residual 120.44 127.48 -7.04 1.30e+00 5.92e-01 2.93e+01 angle pdb=" C SER A 250 " pdb=" N GLN A 251 " pdb=" CA GLN A 251 " ideal model delta sigma weight residual 120.44 127.35 -6.91 1.30e+00 5.92e-01 2.83e+01 angle pdb=" C LYS B 238 " pdb=" N GLN B 239 " pdb=" CA GLN B 239 " ideal model delta sigma weight residual 120.28 127.12 -6.84 1.34e+00 5.57e-01 2.61e+01 ... (remaining 10717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 2475 18.31 - 36.62: 155 36.62 - 54.94: 59 54.94 - 73.25: 40 73.25 - 91.56: 7 Dihedral angle restraints: 2736 sinusoidal: 1546 harmonic: 1190 Sorted by residual: dihedral pdb=" CA PRO B 322 " pdb=" C PRO B 322 " pdb=" N THR B 323 " pdb=" CA THR B 323 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PRO A 322 " pdb=" C PRO A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLU B 179 " pdb=" C GLU B 179 " pdb=" N PRO B 180 " pdb=" CA PRO B 180 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 2733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 282 0.083 - 0.165: 128 0.165 - 0.247: 20 0.247 - 0.329: 6 0.329 - 0.411: 6 Chirality restraints: 442 Sorted by residual: chirality pdb=" CA GLN B 313 " pdb=" N GLN B 313 " pdb=" C GLN B 313 " pdb=" CB GLN B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA GLN A 251 " pdb=" N GLN A 251 " pdb=" C GLN A 251 " pdb=" CB GLN A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LYS B 161 " pdb=" N LYS B 161 " pdb=" C LYS B 161 " pdb=" CB LYS B 161 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 439 not shown) Planarity restraints: 856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 251 " 0.080 2.00e-02 2.50e+03 4.80e-01 3.46e+03 pdb=" CD GLN A 251 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN A 251 " -0.085 2.00e-02 2.50e+03 pdb=" NE2 GLN A 251 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 251 " 0.824 2.00e-02 2.50e+03 pdb="HE22 GLN A 251 " -0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 313 " 0.301 2.00e-02 2.50e+03 4.16e-01 2.59e+03 pdb=" CD GLN B 313 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN B 313 " -0.290 2.00e-02 2.50e+03 pdb=" NE2 GLN B 313 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 313 " 0.655 2.00e-02 2.50e+03 pdb="HE22 GLN B 313 " -0.658 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 318 " -0.312 2.00e-02 2.50e+03 3.99e-01 2.38e+03 pdb=" CD GLN A 318 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 318 " 0.306 2.00e-02 2.50e+03 pdb=" NE2 GLN A 318 " 0.005 2.00e-02 2.50e+03 pdb="HE21 GLN A 318 " -0.627 2.00e-02 2.50e+03 pdb="HE22 GLN A 318 " 0.607 2.00e-02 2.50e+03 ... (remaining 853 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 304 2.18 - 2.78: 10349 2.78 - 3.39: 16154 3.39 - 3.99: 19956 3.99 - 4.60: 29203 Nonbonded interactions: 75966 Sorted by model distance: nonbonded pdb="HH11 ARG A 247 " pdb=" OE1 GLN B 292 " model vdw 1.570 2.450 nonbonded pdb=" HG SER A 266 " pdb=" OE1 GLU A 335 " model vdw 1.595 2.450 nonbonded pdb=" OE1 GLU B 245 " pdb=" HG1 THR B 249 " model vdw 1.634 2.450 nonbonded pdb=" HG SER B 229 " pdb=" OE1 GLU B 232 " model vdw 1.637 2.450 nonbonded pdb=" O VAL B 206 " pdb=" HG SER B 209 " model vdw 1.653 2.450 ... (remaining 75961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.040 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.140 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.014 0.117 2954 Z= 0.906 Angle : 1.834 8.004 3992 Z= 1.226 Chirality : 0.099 0.411 442 Planarity : 0.016 0.103 518 Dihedral : 14.959 91.559 1150 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.96 % Allowed : 2.88 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.40), residues: 356 helix: -0.79 (0.28), residues: 243 sheet: None (None), residues: 0 loop : 0.03 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.025 TRP A 205 HIS 0.011 0.005 HIS B 219 PHE 0.045 0.014 PHE A 237 TYR 0.142 0.017 TYR B 162 ARG 0.008 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.462 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.7964 (ttp80) cc_final: 0.7437 (ttm170) REVERT: A 306 ASN cc_start: 0.6725 (m-40) cc_final: 0.6311 (p0) REVERT: B 291 ASP cc_start: 0.7782 (p0) cc_final: 0.7415 (p0) outliers start: 3 outliers final: 1 residues processed: 156 average time/residue: 0.5615 time to fit residues: 96.5997 Evaluate side-chains 104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150877 restraints weight = 13308.313| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 4.22 r_work: 0.3713 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2954 Z= 0.234 Angle : 0.644 5.150 3992 Z= 0.345 Chirality : 0.037 0.154 442 Planarity : 0.006 0.043 518 Dihedral : 5.736 22.767 395 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 10.90 % Favored : 87.18 % 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 (0.43), residues: 356 helix: 0.66 (0.31), residues: 248 sheet: None (None), residues: 0 loop : 0.13 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 184 HIS 0.002 0.001 HIS A 219 PHE 0.013 0.002 PHE A 181 TYR 0.011 0.002 TYR B 162 ARG 0.005 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.489 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: A 161 LYS cc_start: 0.6756 (tttt) cc_final: 0.6368 (pptt) REVERT: A 218 MET cc_start: 0.9261 (tpp) cc_final: 0.8936 (tpt) REVERT: A 235 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8815 (mm-30) REVERT: A 256 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7402 (ttm170) REVERT: A 292 GLN cc_start: 0.8757 (mt0) cc_final: 0.8488 (tp-100) REVERT: B 197 ILE cc_start: 0.7993 (mm) cc_final: 0.7456 (tp) REVERT: B 211 ARG cc_start: 0.7859 (ptt90) cc_final: 0.6148 (mmt-90) REVERT: B 263 GLU cc_start: 0.7287 (tt0) cc_final: 0.6993 (tt0) REVERT: B 268 TYR cc_start: 0.8017 (t80) cc_final: 0.7556 (t80) REVERT: B 291 ASP cc_start: 0.8222 (p0) cc_final: 0.7794 (p0) REVERT: B 313 GLN cc_start: 0.8329 (tt0) cc_final: 0.7879 (tp-100) outliers start: 6 outliers final: 3 residues processed: 110 average time/residue: 0.4071 time to fit residues: 51.3003 Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157941 restraints weight = 13148.970| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 4.23 r_work: 0.3721 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2954 Z= 0.165 Angle : 0.558 5.221 3992 Z= 0.294 Chirality : 0.036 0.154 442 Planarity : 0.005 0.049 518 Dihedral : 5.001 19.305 394 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 13.78 % Favored : 84.62 % 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: 1.21 (0.44), residues: 356 helix: 1.11 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.34 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.002 0.001 HIS B 219 PHE 0.011 0.001 PHE A 181 TYR 0.012 0.001 TYR B 254 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.551 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: A 161 LYS cc_start: 0.6854 (tttt) cc_final: 0.6389 (pptt) REVERT: A 218 MET cc_start: 0.9217 (tpp) cc_final: 0.8820 (tpt) REVERT: A 256 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7307 (ttm170) REVERT: A 263 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 197 ILE cc_start: 0.8090 (mm) cc_final: 0.7559 (tp) REVERT: B 211 ARG cc_start: 0.7786 (ptt90) cc_final: 0.6301 (mmt180) REVERT: B 259 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7867 (tt0) REVERT: B 291 ASP cc_start: 0.8101 (p0) cc_final: 0.7653 (p0) REVERT: B 303 ASN cc_start: 0.6833 (m-40) cc_final: 0.6507 (m-40) outliers start: 5 outliers final: 3 residues processed: 108 average time/residue: 0.4045 time to fit residues: 50.0010 Evaluate side-chains 99 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.180673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149197 restraints weight = 13443.075| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 4.22 r_work: 0.3671 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2954 Z= 0.239 Angle : 0.577 5.206 3992 Z= 0.307 Chirality : 0.036 0.148 442 Planarity : 0.005 0.043 518 Dihedral : 4.788 18.968 394 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.92 % Allowed : 13.46 % Favored : 84.62 % 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: 1.33 (0.44), residues: 356 helix: 1.25 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.24 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 184 HIS 0.002 0.001 HIS A 219 PHE 0.019 0.002 PHE A 181 TYR 0.014 0.002 TYR B 162 ARG 0.009 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.461 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: A 161 LYS cc_start: 0.7380 (tttt) cc_final: 0.6650 (pptt) REVERT: A 177 GLU cc_start: 0.8855 (pt0) cc_final: 0.8356 (pm20) REVERT: A 218 MET cc_start: 0.9161 (tpp) cc_final: 0.8786 (tpt) REVERT: A 256 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7252 (ttm170) REVERT: B 197 ILE cc_start: 0.8126 (mm) cc_final: 0.7603 (tp) REVERT: B 211 ARG cc_start: 0.8109 (ptt90) cc_final: 0.6451 (mmt-90) REVERT: B 291 ASP cc_start: 0.8005 (p0) cc_final: 0.7485 (p0) REVERT: B 296 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8419 (mm-30) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.4073 time to fit residues: 48.7282 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 257 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.183203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.151197 restraints weight = 13325.652| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 4.34 r_work: 0.3696 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2954 Z= 0.158 Angle : 0.517 4.925 3992 Z= 0.270 Chirality : 0.035 0.149 442 Planarity : 0.005 0.037 518 Dihedral : 4.515 18.185 394 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.96 % Allowed : 15.71 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.45), residues: 356 helix: 1.42 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.32 (0.65), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.010 0.001 PHE A 181 TYR 0.007 0.001 TYR B 254 ARG 0.004 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.476 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: A 161 LYS cc_start: 0.7467 (tttt) cc_final: 0.6659 (pptt) REVERT: A 177 GLU cc_start: 0.8838 (pt0) cc_final: 0.8358 (pm20) REVERT: A 190 GLU cc_start: 0.8559 (tt0) cc_final: 0.8327 (tt0) REVERT: A 218 MET cc_start: 0.9158 (tpp) cc_final: 0.8711 (tpt) REVERT: A 256 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7241 (ttm170) REVERT: A 314 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8482 (tt0) REVERT: B 197 ILE cc_start: 0.8057 (mm) cc_final: 0.7523 (tp) REVERT: B 211 ARG cc_start: 0.8128 (ptt90) cc_final: 0.6357 (mmt180) REVERT: B 291 ASP cc_start: 0.7956 (p0) cc_final: 0.7433 (p0) outliers start: 3 outliers final: 2 residues processed: 110 average time/residue: 0.3772 time to fit residues: 48.0467 Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.181908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150419 restraints weight = 13132.535| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 4.20 r_work: 0.3690 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2954 Z= 0.176 Angle : 0.531 5.337 3992 Z= 0.274 Chirality : 0.036 0.146 442 Planarity : 0.005 0.047 518 Dihedral : 4.337 17.954 394 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.28 % Allowed : 15.06 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.45), residues: 356 helix: 1.51 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.26 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.005 0.001 PHE A 241 TYR 0.009 0.001 TYR B 162 ARG 0.010 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.431 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: A 161 LYS cc_start: 0.7614 (tttt) cc_final: 0.6813 (pptt) REVERT: A 162 TYR cc_start: 0.7332 (m-80) cc_final: 0.6140 (m-80) REVERT: A 256 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7191 (ttm170) REVERT: A 263 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7285 (tt0) REVERT: A 264 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7991 (ttpt) REVERT: B 197 ILE cc_start: 0.8028 (mm) cc_final: 0.7504 (tp) outliers start: 4 outliers final: 0 residues processed: 96 average time/residue: 0.3512 time to fit residues: 39.6086 Evaluate side-chains 87 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.181153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148990 restraints weight = 13314.601| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 4.27 r_work: 0.3663 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2954 Z= 0.191 Angle : 0.534 7.889 3992 Z= 0.276 Chirality : 0.036 0.203 442 Planarity : 0.005 0.029 518 Dihedral : 4.273 18.135 394 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.96 % Allowed : 16.03 % Favored : 83.01 % 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: 1.70 (0.45), residues: 356 helix: 1.58 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.23 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.016 0.001 PHE A 181 TYR 0.009 0.001 TYR B 162 ARG 0.007 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.855 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: A 161 LYS cc_start: 0.7722 (tttt) cc_final: 0.6773 (pptt) REVERT: A 162 TYR cc_start: 0.7418 (m-80) cc_final: 0.6156 (m-80) REVERT: A 218 MET cc_start: 0.9157 (tpp) cc_final: 0.8660 (tpt) REVERT: A 235 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 256 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7144 (ttm170) REVERT: A 263 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7305 (tt0) REVERT: A 264 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7990 (ttpt) REVERT: B 162 TYR cc_start: 0.7339 (t80) cc_final: 0.4753 (t80) REVERT: B 197 ILE cc_start: 0.8065 (mm) cc_final: 0.7543 (tp) outliers start: 3 outliers final: 2 residues processed: 96 average time/residue: 0.5657 time to fit residues: 65.2394 Evaluate side-chains 92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.181690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150541 restraints weight = 12799.999| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.08 r_work: 0.3679 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2954 Z= 0.176 Angle : 0.528 7.117 3992 Z= 0.272 Chirality : 0.036 0.181 442 Planarity : 0.006 0.057 518 Dihedral : 4.154 17.671 394 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.64 % Allowed : 16.99 % Favored : 82.37 % 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: 1.80 (0.45), residues: 356 helix: 1.68 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.18 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.011 0.001 PHE A 181 TYR 0.008 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.452 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: A 161 LYS cc_start: 0.7738 (tttt) cc_final: 0.6752 (pptt) REVERT: A 162 TYR cc_start: 0.7428 (m-80) cc_final: 0.6158 (m-80) REVERT: A 208 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8526 (tm-30) REVERT: A 218 MET cc_start: 0.9141 (tpp) cc_final: 0.8656 (tpt) REVERT: A 235 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 256 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7151 (ttm170) REVERT: A 264 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8070 (ttpt) REVERT: B 162 TYR cc_start: 0.7384 (t80) cc_final: 0.4308 (p90) REVERT: B 197 ILE cc_start: 0.8045 (mm) cc_final: 0.7404 (tp) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.3973 time to fit residues: 44.5076 Evaluate side-chains 87 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.182541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149814 restraints weight = 13294.111| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 4.41 r_work: 0.3676 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2954 Z= 0.155 Angle : 0.514 7.136 3992 Z= 0.263 Chirality : 0.036 0.175 442 Planarity : 0.005 0.042 518 Dihedral : 3.990 17.209 394 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.32 % Allowed : 17.95 % Favored : 81.73 % 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: 1.93 (0.45), residues: 356 helix: 1.76 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.27 (0.64), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.001 0.000 HIS B 219 PHE 0.008 0.001 PHE A 181 TYR 0.006 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.560 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: A 161 LYS cc_start: 0.7693 (tttt) cc_final: 0.6716 (pptt) REVERT: A 162 TYR cc_start: 0.7366 (m-80) cc_final: 0.6143 (m-80) REVERT: A 208 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8428 (tm-30) REVERT: A 218 MET cc_start: 0.9151 (tpp) cc_final: 0.8662 (tpt) REVERT: A 235 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 256 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7090 (ttm170) REVERT: A 263 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7347 (tt0) REVERT: A 264 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7843 (ttpt) REVERT: B 162 TYR cc_start: 0.7351 (t80) cc_final: 0.4281 (p90) REVERT: B 197 ILE cc_start: 0.7999 (mm) cc_final: 0.7730 (tp) REVERT: B 283 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6736 (tpp80) REVERT: B 292 GLN cc_start: 0.8911 (mt0) cc_final: 0.8444 (tp40) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.3961 time to fit residues: 42.3276 Evaluate side-chains 90 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.179440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148106 restraints weight = 13349.748| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 4.22 r_work: 0.3670 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2954 Z= 0.181 Angle : 0.530 6.765 3992 Z= 0.272 Chirality : 0.035 0.165 442 Planarity : 0.005 0.042 518 Dihedral : 3.954 17.487 394 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.64 % Allowed : 17.95 % Favored : 81.41 % 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: 1.90 (0.45), residues: 356 helix: 1.76 (0.33), residues: 249 sheet: None (None), residues: 0 loop : 0.21 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.014 0.001 PHE A 181 TYR 0.009 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.428 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: A 161 LYS cc_start: 0.7827 (tttt) cc_final: 0.6826 (pptt) REVERT: A 162 TYR cc_start: 0.7511 (m-80) cc_final: 0.6193 (m-80) REVERT: A 218 MET cc_start: 0.9163 (tpp) cc_final: 0.8626 (tpt) REVERT: A 256 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7109 (ttm170) REVERT: A 263 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7397 (tt0) REVERT: A 264 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7876 (ttpt) REVERT: B 162 TYR cc_start: 0.7539 (t80) cc_final: 0.4436 (p90) REVERT: B 197 ILE cc_start: 0.8008 (mm) cc_final: 0.7457 (tp) REVERT: B 283 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6787 (tpp80) REVERT: B 292 GLN cc_start: 0.8911 (mt0) cc_final: 0.8460 (tp40) outliers start: 2 outliers final: 1 residues processed: 90 average time/residue: 0.4579 time to fit residues: 48.1193 Evaluate side-chains 88 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.180919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147685 restraints weight = 13415.202| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 4.46 r_work: 0.3659 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.7628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2954 Z= 0.192 Angle : 0.549 6.668 3992 Z= 0.285 Chirality : 0.036 0.165 442 Planarity : 0.005 0.041 518 Dihedral : 4.092 17.934 394 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.64 % Allowed : 17.63 % Favored : 81.73 % 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: 1.89 (0.45), residues: 356 helix: 1.75 (0.33), residues: 250 sheet: None (None), residues: 0 loop : 0.18 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.001 HIS B 219 PHE 0.014 0.001 PHE A 181 TYR 0.009 0.001 TYR B 162 ARG 0.006 0.001 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.43 seconds wall clock time: 65 minutes 6.59 seconds (3906.59 seconds total)