Starting phenix.real_space_refine on Tue Jan 14 05:25:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb7_19027/01_2025/8rb7_19027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb7_19027/01_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_19027/01_2025/8rb7_19027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb7_19027/01_2025/8rb7_19027.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb7_19027/01_2025/8rb7_19027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb7_19027/01_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-5571/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: 3.19, per 1000 atoms: 0.55 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: 1.42 Conformation dependent library (CDL) restraints added in 373.0 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: 0.33 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: 1.85 Time building geometry restraints manager: 1.66 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: 0.710 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- 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 : 0.439 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: 0.5694 time to fit residues: 97.6364 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 : 0.497 ------------------------------------------------------------------------------- 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 = 0.150878 restraints weight = 13308.316| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 4.22 r_work: 0.3713 rms_B_bonded: 4.71 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 : 0.429 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: 0.8016 (t80) cc_final: 0.7556 (t80) REVERT: B 291 ASP cc_start: 0.8221 (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: 0.4190 time to fit residues: 52.5797 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 : 0.493 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.181092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149735 restraints weight = 13266.927| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 4.27 r_work: 0.3677 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2954 Z= 0.243 Angle : 0.602 5.323 3992 Z= 0.321 Chirality : 0.037 0.154 442 Planarity : 0.005 0.046 518 Dihedral : 5.089 20.023 394 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.92 % Allowed : 13.78 % Favored : 84.29 % 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: 1.14 (0.44), residues: 356 helix: 1.05 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.33 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 184 HIS 0.002 0.001 HIS B 219 PHE 0.019 0.002 PHE A 181 TYR 0.015 0.002 TYR B 162 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 112 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.441 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: 0.7278 (tttt) cc_final: 0.6565 (pptt) REVERT: A 162 TYR cc_start: 0.7007 (m-80) cc_final: 0.6020 (m-80) REVERT: A 218 MET cc_start: 0.9201 (tpp) cc_final: 0.8780 (tpt) REVERT: A 256 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7282 (ttm170) REVERT: A 263 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7372 (mt-10) REVERT: B 197 ILE cc_start: 0.8110 (mm) cc_final: 0.7556 (tp) REVERT: B 211 ARG cc_start: 0.7956 (ptt90) cc_final: 0.6444 (mmt-90) REVERT: B 259 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7632 (tt0) REVERT: B 263 GLU cc_start: 0.7395 (tt0) cc_final: 0.7193 (tt0) REVERT: B 268 TYR cc_start: 0.7972 (t80) cc_final: 0.7507 (t80) REVERT: B 291 ASP cc_start: 0.8034 (p0) cc_final: 0.7569 (p0) outliers start: 6 outliers final: 4 residues processed: 109 average time/residue: 0.4671 time to fit residues: 57.5005 Evaluate side-chains 93 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.184943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151775 restraints weight = 13652.235| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.54 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2954 Z= 0.154 Angle : 0.530 5.207 3992 Z= 0.276 Chirality : 0.035 0.148 442 Planarity : 0.005 0.054 518 Dihedral : 4.687 17.944 394 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.28 % Allowed : 12.50 % Favored : 86.22 % 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: 1.41 (0.45), residues: 356 helix: 1.26 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.39 (0.66), residues: 108 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 0.006 0.001 PHE A 181 TYR 0.008 0.001 TYR B 254 ARG 0.008 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 105 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.458 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: 0.7150 (tttt) cc_final: 0.6505 (pptt) REVERT: A 162 TYR cc_start: 0.6510 (m-80) cc_final: 0.5667 (m-80) REVERT: A 177 GLU cc_start: 0.8837 (pt0) cc_final: 0.8338 (pm20) REVERT: A 218 MET cc_start: 0.9071 (tpp) cc_final: 0.8680 (tpt) REVERT: A 256 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7235 (ttm170) REVERT: B 197 ILE cc_start: 0.8031 (mm) cc_final: 0.7482 (tp) REVERT: B 211 ARG cc_start: 0.7693 (ptt90) cc_final: 0.6232 (mmt180) REVERT: B 291 ASP cc_start: 0.7876 (p0) cc_final: 0.7373 (p0) outliers start: 4 outliers final: 2 residues processed: 102 average time/residue: 0.4234 time to fit residues: 49.1523 Evaluate side-chains 101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 191 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.179346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148059 restraints weight = 13099.156| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.14 r_work: 0.3658 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2954 Z= 0.225 Angle : 0.544 5.101 3992 Z= 0.288 Chirality : 0.036 0.145 442 Planarity : 0.005 0.030 518 Dihedral : 4.547 18.680 394 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.96 % Allowed : 15.06 % Favored : 83.97 % 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: 1.46 (0.45), residues: 356 helix: 1.34 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.30 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.002 0.001 HIS A 219 PHE 0.019 0.001 PHE A 181 TYR 0.013 0.002 TYR B 162 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 106 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7636 (tttt) cc_final: 0.6828 (pptt) REVERT: A 162 TYR cc_start: 0.7373 (m-80) cc_final: 0.6086 (m-80) REVERT: A 190 GLU cc_start: 0.8643 (tt0) cc_final: 0.8378 (tt0) REVERT: A 256 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7250 (ttm170) REVERT: A 264 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8133 (ttpt) REVERT: A 314 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8475 (tt0) REVERT: B 197 ILE cc_start: 0.8076 (mm) cc_final: 0.7582 (tp) REVERT: B 211 ARG cc_start: 0.8224 (ptt90) cc_final: 0.6532 (mmt180) REVERT: B 263 GLU cc_start: 0.7728 (tt0) cc_final: 0.7434 (tt0) REVERT: B 268 TYR cc_start: 0.7908 (t80) cc_final: 0.7613 (t80) outliers start: 3 outliers final: 2 residues processed: 103 average time/residue: 0.4064 time to fit residues: 47.9751 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 : 0.506 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.175658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143809 restraints weight = 13131.428| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.16 r_work: 0.3616 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2954 Z= 0.305 Angle : 0.597 4.979 3992 Z= 0.319 Chirality : 0.038 0.148 442 Planarity : 0.005 0.029 518 Dihedral : 4.660 19.546 394 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.24 % Allowed : 12.18 % Favored : 85.58 % 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: 1.07 (0.44), residues: 356 helix: 1.05 (0.32), residues: 248 sheet: None (None), residues: 0 loop : 0.14 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 184 HIS 0.002 0.001 HIS A 219 PHE 0.021 0.002 PHE A 181 TYR 0.012 0.002 TYR A 254 ARG 0.003 0.000 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 102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.486 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: 0.7848 (tttt) cc_final: 0.6840 (pptt) REVERT: A 162 TYR cc_start: 0.7575 (m-80) cc_final: 0.6237 (m-80) REVERT: A 218 MET cc_start: 0.9171 (tpp) cc_final: 0.8712 (tpt) REVERT: A 235 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8776 (mm-30) REVERT: A 256 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7214 (ttm170) REVERT: A 263 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 162 TYR cc_start: 0.7653 (t80) cc_final: 0.4525 (p90) REVERT: B 211 ARG cc_start: 0.8438 (ptt90) cc_final: 0.6722 (mmt180) REVERT: B 292 GLN cc_start: 0.9021 (mt0) cc_final: 0.8131 (mp10) outliers start: 7 outliers final: 4 residues processed: 98 average time/residue: 0.4483 time to fit residues: 49.8561 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 : 0.453 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.178616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147104 restraints weight = 12976.702| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.13 r_work: 0.3654 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2954 Z= 0.187 Angle : 0.537 8.250 3992 Z= 0.278 Chirality : 0.037 0.221 442 Planarity : 0.005 0.030 518 Dihedral : 4.443 18.801 394 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.28 % Allowed : 13.78 % Favored : 84.94 % 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: 1.35 (0.45), residues: 356 helix: 1.26 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.24 (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 0.010 0.001 PHE A 181 TYR 0.008 0.001 TYR B 162 ARG 0.003 0.000 ARG B 311 *********************** 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 106 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.450 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: 0.7818 (tttt) cc_final: 0.6786 (pptt) REVERT: A 162 TYR cc_start: 0.7458 (m-80) cc_final: 0.6104 (m-80) REVERT: A 218 MET cc_start: 0.9161 (tpp) cc_final: 0.8659 (tpt) REVERT: A 235 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 256 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7170 (ttm170) REVERT: A 263 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7436 (tt0) REVERT: A 264 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8062 (ttpt) REVERT: B 162 TYR cc_start: 0.7533 (t80) cc_final: 0.4438 (p90) REVERT: B 292 GLN cc_start: 0.8961 (mt0) cc_final: 0.8086 (mp10) outliers start: 4 outliers final: 1 residues processed: 103 average time/residue: 0.4730 time to fit residues: 55.8392 Evaluate side-chains 93 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU 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: 7.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.181921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150767 restraints weight = 12850.129| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 4.11 r_work: 0.3668 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.7440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2954 Z= 0.184 Angle : 0.539 7.233 3992 Z= 0.279 Chirality : 0.037 0.180 442 Planarity : 0.005 0.044 518 Dihedral : 4.271 18.602 394 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.64 % Allowed : 15.71 % 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: 1.44 (0.45), residues: 356 helix: 1.36 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.18 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.001 0.001 HIS B 219 PHE 0.004 0.001 PHE B 237 TYR 0.008 0.001 TYR B 162 ARG 0.005 0.000 ARG A 278 *********************** 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 102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.439 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: 0.7859 (tttt) cc_final: 0.6808 (pptt) REVERT: A 162 TYR cc_start: 0.7506 (m-80) cc_final: 0.6116 (m-80) REVERT: A 190 GLU cc_start: 0.8579 (tt0) cc_final: 0.8224 (tt0) REVERT: A 218 MET cc_start: 0.9150 (tpp) cc_final: 0.8658 (tpt) REVERT: A 235 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8718 (mm-30) REVERT: A 256 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7137 (ttm170) REVERT: A 264 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8140 (ttpt) REVERT: B 162 TYR cc_start: 0.7611 (t80) cc_final: 0.4487 (p90) REVERT: B 211 ARG cc_start: 0.8421 (ptt90) cc_final: 0.6736 (mmt180) REVERT: B 283 ARG cc_start: 0.7326 (ttm110) cc_final: 0.6641 (tpp80) REVERT: B 292 GLN cc_start: 0.8958 (mt0) cc_final: 0.8054 (mp10) outliers start: 2 outliers final: 0 residues processed: 101 average time/residue: 0.4230 time to fit residues: 48.5414 Evaluate side-chains 89 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.184300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152300 restraints weight = 13175.832| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 4.30 r_work: 0.3686 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.7547 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= 0.160 Angle : 0.522 6.925 3992 Z= 0.267 Chirality : 0.036 0.189 442 Planarity : 0.005 0.055 518 Dihedral : 4.081 17.803 394 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.60 % Allowed : 14.74 % 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: 1.68 (0.45), residues: 356 helix: 1.56 (0.33), residues: 248 sheet: None (None), residues: 0 loop : 0.21 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 184 HIS 0.001 0.000 HIS B 219 PHE 0.005 0.001 PHE B 237 TYR 0.005 0.001 TYR B 162 ARG 0.012 0.001 ARG B 287 *********************** 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 104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.544 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: 0.7826 (tttt) cc_final: 0.6773 (pptt) REVERT: A 162 TYR cc_start: 0.7463 (m-80) cc_final: 0.6815 (m-80) REVERT: A 190 GLU cc_start: 0.8624 (tt0) cc_final: 0.8298 (tt0) REVERT: A 208 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8556 (tm-30) REVERT: A 218 MET cc_start: 0.9167 (tpp) cc_final: 0.8717 (tpt) REVERT: A 256 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7127 (ttm170) REVERT: A 263 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7485 (tt0) REVERT: A 264 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7845 (ttpt) REVERT: B 162 TYR cc_start: 0.7527 (t80) cc_final: 0.4459 (p90) REVERT: B 283 ARG cc_start: 0.7327 (ttm110) cc_final: 0.6707 (tpp80) REVERT: B 292 GLN cc_start: 0.8914 (mt0) cc_final: 0.8425 (tp40) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.3752 time to fit residues: 45.4413 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.178921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146794 restraints weight = 13061.119| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.22 r_work: 0.3650 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2954 Z= 0.196 Angle : 0.541 6.520 3992 Z= 0.281 Chirality : 0.036 0.183 442 Planarity : 0.005 0.056 518 Dihedral : 4.083 18.186 394 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.60 % Allowed : 15.06 % 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: 1.63 (0.45), residues: 356 helix: 1.52 (0.33), residues: 250 sheet: None (None), residues: 0 loop : 0.18 (0.64), residues: 106 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 0.012 0.001 ARG B 287 ********************** 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 102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 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: A 161 LYS cc_start: 0.7895 (tttt) cc_final: 0.6833 (pptt) REVERT: A 162 TYR cc_start: 0.7506 (m-80) cc_final: 0.6107 (m-80) REVERT: A 190 GLU cc_start: 0.8657 (tt0) cc_final: 0.8339 (tt0) REVERT: A 218 MET cc_start: 0.9154 (tpp) cc_final: 0.8686 (tpt) REVERT: A 235 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8705 (mm-30) REVERT: A 256 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7145 (ttm170) REVERT: A 263 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7523 (tt0) REVERT: A 264 LYS cc_start: 0.8480 (mtmt) cc_final: 0.7971 (ttpt) REVERT: B 162 TYR cc_start: 0.7654 (t80) cc_final: 0.4494 (p90) REVERT: B 283 ARG cc_start: 0.7520 (ttm110) cc_final: 0.6918 (tpp80) REVERT: B 292 GLN cc_start: 0.8928 (mt0) cc_final: 0.8062 (mp10) outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.4256 time to fit residues: 49.0102 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 167 ILE 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: 3.9990 chunk 34 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 overall best weight: 1.2504 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.183914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152567 restraints weight = 12900.506| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 4.13 r_work: 0.3681 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2954 Z= 0.166 Angle : 0.532 6.646 3992 Z= 0.272 Chirality : 0.036 0.180 442 Planarity : 0.005 0.053 518 Dihedral : 3.994 17.663 394 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.55 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: 1.73 (0.45), residues: 356 helix: 1.59 (0.33), residues: 250 sheet: None (None), residues: 0 loop : 0.23 (0.65), residues: 106 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 0.009 0.001 PHE A 181 TYR 0.006 0.001 TYR B 162 ARG 0.011 0.001 ARG B 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.93 seconds wall clock time: 59 minutes 42.59 seconds (3582.59 seconds total)