Starting phenix.real_space_refine on Fri Aug 22 18:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.map" model { file = "/net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2m_35950/08_2025/8j2m_35950.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 P 2 5.49 5 S 22 5.16 5 C 4376 2.51 5 N 1038 2.21 5 O 1136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6574 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3244 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 9, 'TRANS': 414} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.94, per 1000 atoms: 0.30 Number of scatterers: 6574 At special positions: 0 Unit cell: (104.94, 72.08, 69.96, 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 22 16.00 P 2 15.00 O 1136 8.00 N 1038 7.00 C 4376 6.00 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: 0.60 Conformation dependent library (CDL) restraints added in 442.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 4.115A pdb=" N VAL A 12 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.781A pdb=" N ALA A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.585A pdb=" N GLY A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.932A pdb=" N PHE A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.518A pdb=" N MET A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 109 removed outlier: 4.528A pdb=" N LYS A 99 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 192 removed outlier: 3.746A pdb=" N SER A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 229 removed outlier: 3.685A pdb=" N SER A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 229 " --> pdb=" O TRP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 removed outlier: 3.564A pdb=" N PHE A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.750A pdb=" N ALA A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 315 removed outlier: 3.885A pdb=" N GLN A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 removed outlier: 4.442A pdb=" N TRP A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 360 through 369 Processing helix chain 'A' and resid 374 through 390 removed outlier: 3.632A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 428 removed outlier: 3.501A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 4.115A pdb=" N VAL B 12 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.781A pdb=" N ALA B 39 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.586A pdb=" N GLY B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.932A pdb=" N PHE B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 removed outlier: 3.518A pdb=" N MET B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.528A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 127 Processing helix chain 'B' and resid 132 through 143 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 192 removed outlier: 3.747A pdb=" N SER B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 229 removed outlier: 3.685A pdb=" N SER B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 229 " --> pdb=" O TRP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 removed outlier: 3.564A pdb=" N PHE B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B 249 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.750A pdb=" N ALA B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 315 removed outlier: 3.885A pdb=" N GLN B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 removed outlier: 4.442A pdb=" N TRP B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 360 through 369 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.632A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 428 removed outlier: 3.500A pdb=" N PHE B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1560 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: 0.96 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 998 1.29 - 1.42: 1752 1.42 - 1.55: 3920 1.55 - 1.68: 6 1.68 - 1.81: 42 Bond restraints: 6718 Sorted by residual: bond pdb=" C MET B 174 " pdb=" O MET B 174 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.29e-02 6.01e+03 3.14e+01 bond pdb=" C MET A 174 " pdb=" O MET A 174 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.29e-02 6.01e+03 3.14e+01 bond pdb=" N PRO A 148 " pdb=" CD PRO A 148 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" N HIS B 323 " pdb=" CA HIS B 323 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.22e-02 6.72e+03 1.55e+01 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 7934 1.99 - 3.98: 994 3.98 - 5.98: 150 5.98 - 7.97: 24 7.97 - 9.96: 12 Bond angle restraints: 9114 Sorted by residual: angle pdb=" N THR B 422 " pdb=" CA THR B 422 " pdb=" C THR B 422 " ideal model delta sigma weight residual 111.71 102.71 9.00 1.15e+00 7.56e-01 6.13e+01 angle pdb=" N THR A 422 " pdb=" CA THR A 422 " pdb=" C THR A 422 " ideal model delta sigma weight residual 111.71 102.72 8.99 1.15e+00 7.56e-01 6.12e+01 angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 110.42 103.75 6.67 9.60e-01 1.09e+00 4.83e+01 angle pdb=" N ILE A 339 " pdb=" CA ILE A 339 " pdb=" C ILE A 339 " ideal model delta sigma weight residual 110.42 103.77 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N MET B 402 " pdb=" CA MET B 402 " pdb=" C MET B 402 " ideal model delta sigma weight residual 111.11 118.91 -7.80 1.20e+00 6.94e-01 4.23e+01 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 3736 33.80 - 67.59: 116 67.59 - 101.39: 20 101.39 - 135.18: 2 135.18 - 168.98: 6 Dihedral angle restraints: 3880 sinusoidal: 1478 harmonic: 2402 Sorted by residual: dihedral pdb=" C PHE A 302 " pdb=" N PHE A 302 " pdb=" CA PHE A 302 " pdb=" CB PHE A 302 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" C PHE B 302 " pdb=" N PHE B 302 " pdb=" CA PHE B 302 " pdb=" CB PHE B 302 " ideal model delta harmonic sigma weight residual -122.60 -135.99 13.39 0 2.50e+00 1.60e-01 2.87e+01 dihedral pdb=" N HIS A 427 " pdb=" C HIS A 427 " pdb=" CA HIS A 427 " pdb=" CB HIS A 427 " ideal model delta harmonic sigma weight residual 122.80 134.31 -11.51 0 2.50e+00 1.60e-01 2.12e+01 ... (remaining 3877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 855 0.083 - 0.165: 189 0.165 - 0.248: 42 0.248 - 0.330: 8 0.330 - 0.413: 6 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA PHE A 302 " pdb=" N PHE A 302 " pdb=" C PHE A 302 " pdb=" CB PHE A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA PHE B 302 " pdb=" N PHE B 302 " pdb=" C PHE B 302 " pdb=" CB PHE B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA HIS A 427 " pdb=" N HIS A 427 " pdb=" C HIS A 427 " pdb=" CB HIS A 427 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1097 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 316 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C ASN A 316 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 316 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 317 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 316 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C ASN B 316 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 316 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 317 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 297 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ALA A 297 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 297 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 298 " 0.015 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 118 2.68 - 3.23: 6745 3.23 - 3.79: 10306 3.79 - 4.34: 13785 4.34 - 4.90: 22473 Nonbonded interactions: 53427 Sorted by model distance: nonbonded pdb=" O THR B 146 " pdb=" OD1 ASP B 147 " model vdw 2.121 3.040 nonbonded pdb=" O THR A 146 " pdb=" OD1 ASP A 147 " model vdw 2.122 3.040 nonbonded pdb=" O GLY B 140 " pdb=" OG SER B 144 " model vdw 2.267 3.040 nonbonded pdb=" O GLY A 140 " pdb=" OG SER A 144 " model vdw 2.267 3.040 nonbonded pdb=" O PHE A 118 " pdb=" OG SER A 121 " model vdw 2.317 3.040 ... (remaining 53422 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: 0.01 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: 1.320 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.009 0.072 6718 Z= 0.638 Angle : 1.363 9.961 9114 Z= 1.008 Chirality : 0.079 0.413 1100 Planarity : 0.006 0.057 1098 Dihedral : 18.826 168.976 2344 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 9.45 % Favored : 87.65 % Cbeta Deviations : 1.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.26), residues: 844 helix: -1.02 (0.18), residues: 678 sheet: None (None), residues: 0 loop : -1.90 (0.37), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.014 0.002 TYR B 183 PHE 0.015 0.002 PHE A 405 TRP 0.020 0.002 TRP A 68 HIS 0.005 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00921 ( 6718) covalent geometry : angle 1.36277 ( 9114) hydrogen bonds : bond 0.18624 ( 520) hydrogen bonds : angle 7.10085 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 288 time to evaluate : 0.139 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 158 LEU cc_start: 0.8126 (mp) cc_final: 0.7900 (mp) REVERT: A 234 ILE cc_start: 0.8150 (mm) cc_final: 0.7774 (mm) REVERT: B 40 LEU cc_start: 0.8452 (mt) cc_final: 0.8240 (mt) REVERT: B 124 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.8058 (tptp) REVERT: B 275 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6843 (mmmt) outliers start: 20 outliers final: 5 residues processed: 299 average time/residue: 0.0613 time to fit residues: 24.3781 Evaluate side-chains 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 175 ASN A 288 HIS A 338 GLN B 56 HIS B 175 ASN B 418 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091296 restraints weight = 15447.894| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.10 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6718 Z= 0.159 Angle : 0.643 6.725 9114 Z= 0.341 Chirality : 0.040 0.123 1100 Planarity : 0.005 0.052 1098 Dihedral : 15.457 178.523 981 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.09 % Allowed : 19.48 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.28), residues: 844 helix: 0.70 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.94 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 188 TYR 0.023 0.002 TYR A 334 PHE 0.032 0.002 PHE B 405 TRP 0.009 0.001 TRP B 68 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6718) covalent geometry : angle 0.64265 ( 9114) hydrogen bonds : bond 0.05542 ( 520) hydrogen bonds : angle 4.35652 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.9004 (t0) cc_final: 0.8675 (t0) REVERT: A 156 LYS cc_start: 0.8671 (tppt) cc_final: 0.8414 (mtpp) REVERT: A 171 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 256 GLU cc_start: 0.7696 (mp0) cc_final: 0.7402 (mp0) REVERT: A 268 MET cc_start: 0.8877 (mtt) cc_final: 0.7865 (tmm) REVERT: A 284 GLN cc_start: 0.8265 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 311 ASP cc_start: 0.8960 (t0) cc_final: 0.8179 (t0) REVERT: A 360 ASP cc_start: 0.8602 (m-30) cc_final: 0.8205 (m-30) REVERT: A 363 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: A 423 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7129 (tm-30) REVERT: B 146 THR cc_start: 0.7856 (p) cc_final: 0.7652 (p) REVERT: B 171 GLU cc_start: 0.8612 (tt0) cc_final: 0.8271 (tm-30) REVERT: B 268 MET cc_start: 0.8966 (mtt) cc_final: 0.7878 (tmm) REVERT: B 360 ASP cc_start: 0.8352 (m-30) cc_final: 0.8112 (m-30) REVERT: B 363 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: B 402 MET cc_start: 0.9336 (mmp) cc_final: 0.9072 (mmp) outliers start: 35 outliers final: 23 residues processed: 236 average time/residue: 0.0438 time to fit residues: 15.1462 Evaluate side-chains 199 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 56 HIS ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN B 27 HIS B 288 HIS ** B 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091407 restraints weight = 15684.592| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.01 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6718 Z= 0.155 Angle : 0.634 8.139 9114 Z= 0.329 Chirality : 0.038 0.146 1100 Planarity : 0.004 0.050 1098 Dihedral : 14.014 157.588 972 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.81 % Allowed : 24.85 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.29), residues: 844 helix: 1.21 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.90 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.020 0.002 TYR A 36 PHE 0.011 0.001 PHE B 405 TRP 0.007 0.001 TRP B 68 HIS 0.008 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6718) covalent geometry : angle 0.63351 ( 9114) hydrogen bonds : bond 0.04954 ( 520) hydrogen bonds : angle 4.14597 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.9003 (t0) cc_final: 0.8643 (t0) REVERT: A 156 LYS cc_start: 0.8721 (tppt) cc_final: 0.8454 (mtpp) REVERT: A 157 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 171 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8067 (tm-30) REVERT: A 268 MET cc_start: 0.8871 (mtt) cc_final: 0.8043 (tmm) REVERT: A 363 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: B 142 LEU cc_start: 0.9109 (mt) cc_final: 0.8767 (mt) REVERT: B 163 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8069 (tttt) REVERT: B 171 GLU cc_start: 0.8694 (tt0) cc_final: 0.8241 (tm-30) REVERT: B 189 MET cc_start: 0.9434 (mmm) cc_final: 0.9122 (mmm) REVERT: B 268 MET cc_start: 0.8917 (mtt) cc_final: 0.7895 (tmm) REVERT: B 360 ASP cc_start: 0.8259 (m-30) cc_final: 0.8024 (m-30) REVERT: B 363 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: B 403 PHE cc_start: 0.8588 (m-80) cc_final: 0.8183 (t80) outliers start: 40 outliers final: 19 residues processed: 213 average time/residue: 0.0500 time to fit residues: 15.3636 Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS A 354 HIS A 392 GLN B 56 HIS B 288 HIS B 392 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092662 restraints weight = 15897.636| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.92 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6718 Z= 0.142 Angle : 0.616 7.728 9114 Z= 0.320 Chirality : 0.038 0.151 1100 Planarity : 0.004 0.049 1098 Dihedral : 12.838 134.646 970 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.52 % Allowed : 27.76 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.29), residues: 844 helix: 1.43 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -1.92 (0.43), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.018 0.002 TYR B 295 PHE 0.010 0.001 PHE B 405 TRP 0.011 0.001 TRP A 369 HIS 0.012 0.002 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6718) covalent geometry : angle 0.61606 ( 9114) hydrogen bonds : bond 0.04664 ( 520) hydrogen bonds : angle 4.04652 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 36 TYR cc_start: 0.8441 (t80) cc_final: 0.8106 (t80) REVERT: A 70 ASN cc_start: 0.9030 (t0) cc_final: 0.8645 (t0) REVERT: A 157 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 171 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 189 MET cc_start: 0.9400 (mmm) cc_final: 0.9195 (mmm) REVERT: A 268 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: A 363 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: B 36 TYR cc_start: 0.8345 (t80) cc_final: 0.8105 (t80) REVERT: B 68 TRP cc_start: 0.8771 (m100) cc_final: 0.8454 (m100) REVERT: B 163 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8085 (tttt) REVERT: B 171 GLU cc_start: 0.8713 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 268 MET cc_start: 0.8784 (mtt) cc_final: 0.7979 (tmm) REVERT: B 332 LEU cc_start: 0.9474 (tp) cc_final: 0.8769 (tp) REVERT: B 336 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: B 360 ASP cc_start: 0.8177 (m-30) cc_final: 0.7950 (m-30) REVERT: B 363 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: B 386 ARG cc_start: 0.8712 (mmt90) cc_final: 0.8455 (mmm-85) outliers start: 38 outliers final: 23 residues processed: 206 average time/residue: 0.0438 time to fit residues: 13.2172 Evaluate side-chains 199 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS B 288 HIS B 392 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092139 restraints weight = 16065.985| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 4.12 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6718 Z= 0.148 Angle : 0.630 8.159 9114 Z= 0.323 Chirality : 0.038 0.192 1100 Planarity : 0.004 0.051 1098 Dihedral : 11.880 117.934 970 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.25 % Allowed : 26.16 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.29), residues: 844 helix: 1.46 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.019 0.002 TYR B 36 PHE 0.015 0.001 PHE A 405 TRP 0.008 0.001 TRP B 369 HIS 0.011 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6718) covalent geometry : angle 0.63035 ( 9114) hydrogen bonds : bond 0.04622 ( 520) hydrogen bonds : angle 4.02815 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASN cc_start: 0.8973 (t0) cc_final: 0.8574 (t0) REVERT: A 157 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8912 (tm-30) REVERT: A 171 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 268 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8033 (tmm) REVERT: A 336 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8095 (m-80) REVERT: A 363 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: B 157 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8718 (tm-30) REVERT: B 171 GLU cc_start: 0.8724 (tt0) cc_final: 0.8224 (tm-30) REVERT: B 189 MET cc_start: 0.9483 (mmm) cc_final: 0.9265 (mmm) REVERT: B 236 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7031 (mp0) REVERT: B 268 MET cc_start: 0.8852 (mtt) cc_final: 0.8051 (tmm) REVERT: B 332 LEU cc_start: 0.9484 (tp) cc_final: 0.8767 (tp) REVERT: B 336 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 363 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: B 386 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8435 (mmm-85) outliers start: 43 outliers final: 24 residues processed: 204 average time/residue: 0.0510 time to fit residues: 14.9214 Evaluate side-chains 201 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS B 56 HIS B 288 HIS B 392 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091467 restraints weight = 15596.478| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.01 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6718 Z= 0.159 Angle : 0.653 8.487 9114 Z= 0.328 Chirality : 0.039 0.156 1100 Planarity : 0.004 0.050 1098 Dihedral : 11.257 116.628 970 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.67 % Allowed : 28.63 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.29), residues: 844 helix: 1.46 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.86 (0.43), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.019 0.002 TYR A 36 PHE 0.014 0.001 PHE A 405 TRP 0.006 0.001 TRP B 369 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6718) covalent geometry : angle 0.65276 ( 9114) hydrogen bonds : bond 0.04711 ( 520) hydrogen bonds : angle 4.07375 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8869 (m100) cc_final: 0.8594 (m100) REVERT: A 70 ASN cc_start: 0.9002 (t0) cc_final: 0.8588 (t0) REVERT: A 157 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8918 (tm-30) REVERT: A 171 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 268 MET cc_start: 0.8734 (mtt) cc_final: 0.8057 (tmm) REVERT: A 336 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: A 363 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: B 157 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8739 (tm-30) REVERT: B 171 GLU cc_start: 0.8794 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 189 MET cc_start: 0.9477 (mmm) cc_final: 0.9237 (mmm) REVERT: B 268 MET cc_start: 0.8767 (mtt) cc_final: 0.8061 (tmm) REVERT: B 332 LEU cc_start: 0.9488 (tp) cc_final: 0.8707 (tp) REVERT: B 336 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: B 363 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: B 386 ARG cc_start: 0.8754 (mmt90) cc_final: 0.8426 (mmm-85) REVERT: B 403 PHE cc_start: 0.8656 (m-80) cc_final: 0.8293 (t80) outliers start: 39 outliers final: 25 residues processed: 188 average time/residue: 0.0504 time to fit residues: 13.7407 Evaluate side-chains 191 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS B 288 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090854 restraints weight = 15601.685| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.07 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6718 Z= 0.140 Angle : 0.663 12.116 9114 Z= 0.328 Chirality : 0.038 0.166 1100 Planarity : 0.004 0.053 1098 Dihedral : 10.770 112.582 970 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.51 % Allowed : 29.94 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.29), residues: 844 helix: 1.46 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.88 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.023 0.002 TYR A 36 PHE 0.014 0.001 PHE A 405 TRP 0.004 0.001 TRP A 327 HIS 0.014 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6718) covalent geometry : angle 0.66286 ( 9114) hydrogen bonds : bond 0.04518 ( 520) hydrogen bonds : angle 4.05842 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8876 (m100) cc_final: 0.8599 (m100) REVERT: A 70 ASN cc_start: 0.8965 (t0) cc_final: 0.8163 (t0) REVERT: A 157 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8926 (tm-30) REVERT: A 171 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 268 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7980 (tmm) REVERT: A 336 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: B 104 MET cc_start: 0.8815 (ttm) cc_final: 0.8462 (ttm) REVERT: B 157 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8815 (tm-30) REVERT: B 171 GLU cc_start: 0.8763 (tt0) cc_final: 0.8228 (tm-30) REVERT: B 189 MET cc_start: 0.9502 (mmm) cc_final: 0.9245 (mmm) REVERT: B 268 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7993 (tmm) REVERT: B 332 LEU cc_start: 0.9483 (tp) cc_final: 0.8707 (tp) REVERT: B 336 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8225 (m-80) REVERT: B 363 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: B 386 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8455 (mmm-85) REVERT: B 403 PHE cc_start: 0.8622 (m-80) cc_final: 0.8285 (t80) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.0489 time to fit residues: 14.2112 Evaluate side-chains 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS B 56 HIS B 288 HIS B 316 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093436 restraints weight = 15447.109| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.03 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6718 Z= 0.142 Angle : 0.678 15.173 9114 Z= 0.332 Chirality : 0.040 0.233 1100 Planarity : 0.004 0.056 1098 Dihedral : 10.336 108.541 970 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.65 % Allowed : 31.83 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.29), residues: 844 helix: 1.46 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.027 0.002 TYR B 36 PHE 0.012 0.001 PHE A 405 TRP 0.004 0.001 TRP A 290 HIS 0.007 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6718) covalent geometry : angle 0.67820 ( 9114) hydrogen bonds : bond 0.04460 ( 520) hydrogen bonds : angle 4.07331 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8886 (m100) cc_final: 0.8598 (m100) REVERT: A 70 ASN cc_start: 0.8967 (t0) cc_final: 0.8127 (t0) REVERT: A 157 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8918 (tm-30) REVERT: A 171 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 189 MET cc_start: 0.9325 (mmm) cc_final: 0.9100 (mmm) REVERT: A 268 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7940 (tmm) REVERT: A 336 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: A 426 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 104 MET cc_start: 0.8881 (ttm) cc_final: 0.8515 (ttm) REVERT: B 157 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8834 (tm-30) REVERT: B 171 GLU cc_start: 0.8784 (tt0) cc_final: 0.8198 (tm-30) REVERT: B 189 MET cc_start: 0.9502 (mmm) cc_final: 0.9246 (mmm) REVERT: B 236 GLU cc_start: 0.8136 (mt-10) cc_final: 0.6862 (mp0) REVERT: B 268 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7994 (tmm) REVERT: B 275 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8339 (mttt) REVERT: B 332 LEU cc_start: 0.9488 (tp) cc_final: 0.8707 (tp) REVERT: B 336 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 363 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8298 (pm20) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 0.0477 time to fit residues: 13.9427 Evaluate side-chains 194 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.0770 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS B 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.111031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092859 restraints weight = 15479.022| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.15 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6718 Z= 0.139 Angle : 0.718 15.324 9114 Z= 0.348 Chirality : 0.041 0.260 1100 Planarity : 0.004 0.058 1098 Dihedral : 9.996 104.589 970 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.78 % Allowed : 33.28 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.29), residues: 844 helix: 1.40 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.62 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 322 TYR 0.033 0.002 TYR B 36 PHE 0.009 0.001 PHE A 405 TRP 0.013 0.001 TRP A 327 HIS 0.007 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6718) covalent geometry : angle 0.71826 ( 9114) hydrogen bonds : bond 0.04370 ( 520) hydrogen bonds : angle 4.12784 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8850 (m100) cc_final: 0.8566 (m100) REVERT: A 70 ASN cc_start: 0.8897 (t0) cc_final: 0.8360 (t0) REVERT: A 157 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8931 (tm-30) REVERT: A 171 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 189 MET cc_start: 0.9322 (mmm) cc_final: 0.9064 (mmm) REVERT: A 236 GLU cc_start: 0.7356 (mp0) cc_final: 0.6547 (mp0) REVERT: A 268 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7970 (tmm) REVERT: A 336 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: A 360 ASP cc_start: 0.8749 (m-30) cc_final: 0.8388 (p0) REVERT: A 361 LEU cc_start: 0.8767 (mp) cc_final: 0.8492 (pp) REVERT: A 426 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 104 MET cc_start: 0.8826 (ttm) cc_final: 0.8515 (ttm) REVERT: B 157 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8828 (tm-30) REVERT: B 171 GLU cc_start: 0.8783 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 189 MET cc_start: 0.9493 (mmm) cc_final: 0.9228 (mmm) REVERT: B 236 GLU cc_start: 0.8116 (mt-10) cc_final: 0.6890 (mp0) REVERT: B 268 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7862 (tmm) REVERT: B 275 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8307 (mttt) REVERT: B 332 LEU cc_start: 0.9474 (tp) cc_final: 0.8624 (tp) REVERT: B 336 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: B 363 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: B 403 PHE cc_start: 0.8609 (m-80) cc_final: 0.8320 (t80) outliers start: 26 outliers final: 16 residues processed: 198 average time/residue: 0.0438 time to fit residues: 13.0154 Evaluate side-chains 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS B 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093493 restraints weight = 15480.467| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.08 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6718 Z= 0.150 Angle : 0.730 15.188 9114 Z= 0.355 Chirality : 0.042 0.327 1100 Planarity : 0.004 0.058 1098 Dihedral : 9.837 102.618 970 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.49 % Allowed : 33.28 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.29), residues: 844 helix: 1.39 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -1.46 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.033 0.002 TYR A 36 PHE 0.051 0.001 PHE A 405 TRP 0.008 0.001 TRP B 225 HIS 0.006 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6718) covalent geometry : angle 0.72981 ( 9114) hydrogen bonds : bond 0.04452 ( 520) hydrogen bonds : angle 4.18198 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8863 (m100) cc_final: 0.8578 (m100) REVERT: A 70 ASN cc_start: 0.8938 (t0) cc_final: 0.8072 (t0) REVERT: A 104 MET cc_start: 0.8874 (ttm) cc_final: 0.8600 (ttm) REVERT: A 157 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8911 (tm-30) REVERT: A 171 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 189 MET cc_start: 0.9292 (mmm) cc_final: 0.9021 (mmm) REVERT: A 236 GLU cc_start: 0.7447 (mp0) cc_final: 0.6518 (mp0) REVERT: A 268 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7977 (tmm) REVERT: A 336 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: A 360 ASP cc_start: 0.8785 (m-30) cc_final: 0.8404 (p0) REVERT: A 361 LEU cc_start: 0.8769 (mp) cc_final: 0.8497 (pp) REVERT: A 426 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 104 MET cc_start: 0.8905 (ttm) cc_final: 0.8619 (ttm) REVERT: B 157 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8821 (tm-30) REVERT: B 189 MET cc_start: 0.9477 (mmm) cc_final: 0.9202 (mmm) REVERT: B 268 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: B 275 LYS cc_start: 0.8680 (mmmt) cc_final: 0.8304 (mttt) REVERT: B 332 LEU cc_start: 0.9480 (tp) cc_final: 0.8605 (tp) REVERT: B 336 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: B 363 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: B 403 PHE cc_start: 0.8585 (m-80) cc_final: 0.8352 (t80) outliers start: 24 outliers final: 17 residues processed: 191 average time/residue: 0.0459 time to fit residues: 13.2238 Evaluate side-chains 192 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 288 HIS A 418 ASN B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090739 restraints weight = 15670.098| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.05 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6718 Z= 0.197 Angle : 0.748 13.889 9114 Z= 0.370 Chirality : 0.043 0.295 1100 Planarity : 0.004 0.058 1098 Dihedral : 9.975 104.962 970 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.22 % Allowed : 32.56 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.29), residues: 844 helix: 1.38 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.48 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.033 0.002 TYR A 36 PHE 0.057 0.002 PHE A 320 TRP 0.006 0.001 TRP B 369 HIS 0.007 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 6718) covalent geometry : angle 0.74754 ( 9114) hydrogen bonds : bond 0.04812 ( 520) hydrogen bonds : angle 4.29999 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 931.86 seconds wall clock time: 16 minutes 49.15 seconds (1009.15 seconds total)