Starting phenix.real_space_refine on Thu Nov 14 16:43:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_35950.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_35950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_35950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_35950.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2m_35950/11_2024/8j2m_35950.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 5.78, per 1000 atoms: 0.88 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: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 1.83 Time building geometry restraints manager: 2.13 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: 0.00 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- 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= 0.598 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (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 TRP 0.020 0.002 TRP A 68 HIS 0.005 0.001 HIS B 95 PHE 0.015 0.002 PHE A 405 TYR 0.014 0.002 TYR B 183 ARG 0.002 0.000 ARG A 373 *********************** 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 : 0.731 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: 0.1914 time to fit residues: 75.0060 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 : 0.751 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6718 Z= 0.221 Angle : 0.646 6.657 9114 Z= 0.344 Chirality : 0.040 0.126 1100 Planarity : 0.005 0.052 1098 Dihedral : 15.590 179.855 981 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.09 % Allowed : 19.04 % Favored : 75.87 % 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: 0.30 (0.27), residues: 844 helix: 0.68 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.93 (0.43), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 68 HIS 0.007 0.001 HIS A 427 PHE 0.032 0.002 PHE B 405 TYR 0.023 0.002 TYR A 334 ARG 0.005 0.001 ARG A 188 *********************** 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 250 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.7332 (t0) cc_final: 0.6758 (t0) REVERT: A 360 ASP cc_start: 0.7566 (m-30) cc_final: 0.7266 (m-30) outliers start: 35 outliers final: 23 residues processed: 234 average time/residue: 0.1487 time to fit residues: 49.5596 Evaluate side-chains 194 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 345 VAL 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 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 378 LEU 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 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** B 27 HIS B 56 HIS B 175 ASN B 288 HIS B 392 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6718 Z= 0.220 Angle : 0.654 8.226 9114 Z= 0.340 Chirality : 0.039 0.149 1100 Planarity : 0.004 0.049 1098 Dihedral : 14.178 160.008 972 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.38 % Allowed : 24.56 % Favored : 70.06 % 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: 0.97 (0.28), residues: 844 helix: 1.22 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.87 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 68 HIS 0.007 0.001 HIS B 427 PHE 0.011 0.001 PHE B 405 TYR 0.020 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** 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 226 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 LEU cc_start: 0.8461 (mt) cc_final: 0.7886 (mt) outliers start: 37 outliers final: 20 residues processed: 209 average time/residue: 0.1401 time to fit residues: 41.3329 Evaluate side-chains 190 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 123 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 233 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 345 VAL 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 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 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 75 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6718 Z= 0.220 Angle : 0.650 7.968 9114 Z= 0.334 Chirality : 0.039 0.159 1100 Planarity : 0.004 0.049 1098 Dihedral : 13.177 140.035 970 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.67 % Allowed : 27.18 % Favored : 67.15 % 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: 1.24 (0.29), residues: 844 helix: 1.36 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.60 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 369 HIS 0.012 0.001 HIS A 354 PHE 0.012 0.001 PHE A 405 TYR 0.018 0.002 TYR B 295 ARG 0.002 0.000 ARG A 193 *********************** 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 207 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 336 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7700 (m-80) outliers start: 39 outliers final: 23 residues processed: 188 average time/residue: 0.1381 time to fit residues: 37.3893 Evaluate side-chains 183 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 56 HIS Chi-restraints excluded: chain A residue 149 VAL 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 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 378 LEU 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 336 PHE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 403 PHE 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 67 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6718 Z= 0.192 Angle : 0.650 8.078 9114 Z= 0.333 Chirality : 0.038 0.199 1100 Planarity : 0.004 0.052 1098 Dihedral : 12.040 118.608 970 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.67 % Allowed : 27.03 % Favored : 67.30 % 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 (0.29), residues: 844 helix: 1.47 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.71 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 369 HIS 0.007 0.001 HIS A 427 PHE 0.014 0.001 PHE A 405 TYR 0.021 0.002 TYR B 36 ARG 0.002 0.000 ARG B 386 *********************** 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 225 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: B 336 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7700 (m-80) outliers start: 39 outliers final: 22 residues processed: 206 average time/residue: 0.1374 time to fit residues: 40.4083 Evaluate side-chains 188 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 155 LEU 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 336 PHE Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 38 VAL 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 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 403 PHE 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 27 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6718 Z= 0.206 Angle : 0.682 9.984 9114 Z= 0.340 Chirality : 0.039 0.152 1100 Planarity : 0.004 0.056 1098 Dihedral : 11.227 115.117 970 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.81 % Allowed : 27.91 % Favored : 66.28 % 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: 1.30 (0.29), residues: 844 helix: 1.46 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.80 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 369 HIS 0.006 0.001 HIS A 56 PHE 0.012 0.001 PHE A 320 TYR 0.024 0.002 TYR A 36 ARG 0.002 0.000 ARG A 193 *********************** 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 223 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: B 336 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7685 (m-80) outliers start: 40 outliers final: 24 residues processed: 205 average time/residue: 0.1416 time to fit residues: 41.7657 Evaluate side-chains 182 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 56 HIS Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 223 VAL 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 344 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 403 PHE 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 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6718 Z= 0.218 Angle : 0.728 14.313 9114 Z= 0.358 Chirality : 0.041 0.210 1100 Planarity : 0.004 0.058 1098 Dihedral : 10.898 113.248 970 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.09 % Allowed : 29.80 % Favored : 65.12 % 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 (0.29), residues: 844 helix: 1.46 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.66 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 369 HIS 0.016 0.001 HIS A 56 PHE 0.035 0.001 PHE A 405 TYR 0.020 0.002 TYR A 36 ARG 0.003 0.000 ARG A 322 *********************** 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 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.6361 (mp0) cc_final: 0.6060 (mp0) REVERT: A 336 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: B 336 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 35 outliers final: 22 residues processed: 181 average time/residue: 0.1260 time to fit residues: 32.5949 Evaluate side-chains 183 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 223 VAL 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 344 VAL Chi-restraints excluded: chain B residue 345 VAL 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 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 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 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5370 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= 0.206 Angle : 0.727 14.464 9114 Z= 0.356 Chirality : 0.040 0.228 1100 Planarity : 0.004 0.060 1098 Dihedral : 10.536 110.152 970 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.65 % Allowed : 30.52 % Favored : 64.83 % 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: 1.29 (0.29), residues: 844 helix: 1.41 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.90 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 369 HIS 0.006 0.001 HIS A 56 PHE 0.043 0.001 PHE A 405 TYR 0.019 0.002 TYR B 36 ARG 0.002 0.000 ARG A 193 *********************** 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 201 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 171 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 236 GLU cc_start: 0.6118 (mp0) cc_final: 0.5765 (mp0) REVERT: B 264 MET cc_start: 0.6542 (tmm) cc_final: 0.6298 (tmm) REVERT: B 336 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7624 (m-80) outliers start: 32 outliers final: 24 residues processed: 186 average time/residue: 0.1337 time to fit residues: 36.1554 Evaluate side-chains 187 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 56 HIS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 19 LEU 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 223 VAL 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 344 VAL Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 415 LEU 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 75 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 48 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5490 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= 0.205 Angle : 0.758 14.742 9114 Z= 0.361 Chirality : 0.041 0.292 1100 Planarity : 0.004 0.059 1098 Dihedral : 10.230 107.337 970 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.22 % Allowed : 31.83 % Favored : 63.95 % 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 (0.29), residues: 844 helix: 1.47 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 369 HIS 0.004 0.001 HIS A 56 PHE 0.049 0.001 PHE A 405 TYR 0.024 0.002 TYR B 36 ARG 0.002 0.000 ARG A 193 *********************** 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 205 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 236 GLU cc_start: 0.6383 (mp0) cc_final: 0.6170 (mp0) REVERT: A 336 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: B 264 MET cc_start: 0.6518 (tmm) cc_final: 0.6299 (tmm) REVERT: B 336 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7572 (m-80) outliers start: 29 outliers final: 23 residues processed: 191 average time/residue: 0.1370 time to fit residues: 38.0539 Evaluate side-chains 190 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 56 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 19 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 149 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 223 VAL 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 405 PHE Chi-restraints excluded: chain B residue 415 LEU 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 37 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6718 Z= 0.208 Angle : 0.801 14.645 9114 Z= 0.379 Chirality : 0.043 0.352 1100 Planarity : 0.004 0.060 1098 Dihedral : 9.920 103.695 970 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.20 % Allowed : 33.87 % 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 (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 (0.29), residues: 844 helix: 1.45 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -1.84 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 369 HIS 0.005 0.001 HIS A 56 PHE 0.051 0.001 PHE A 405 TYR 0.023 0.002 TYR B 36 ARG 0.002 0.000 ARG A 193 ********************** 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 197 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 236 GLU cc_start: 0.6352 (mp0) cc_final: 0.6111 (mp0) REVERT: B 236 GLU cc_start: 0.6239 (mp0) cc_final: 0.5993 (mp0) REVERT: B 264 MET cc_start: 0.6484 (tmm) cc_final: 0.6250 (tmm) REVERT: B 336 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7553 (m-80) outliers start: 22 outliers final: 20 residues processed: 185 average time/residue: 0.1325 time to fit residues: 35.3837 Evaluate side-chains 186 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 56 HIS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 19 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 223 VAL 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 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 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 8 optimal weight: 0.0070 chunk 12 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.115047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097380 restraints weight = 15066.289| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.08 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5860 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= 0.200 Angle : 0.797 15.247 9114 Z= 0.375 Chirality : 0.042 0.345 1100 Planarity : 0.004 0.059 1098 Dihedral : 9.613 100.220 970 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.07 % Allowed : 32.27 % Favored : 63.66 % 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: 1.34 (0.29), residues: 844 helix: 1.45 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.90 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 369 HIS 0.003 0.001 HIS B 427 PHE 0.045 0.001 PHE A 405 TYR 0.021 0.002 TYR B 36 ARG 0.002 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1627.96 seconds wall clock time: 34 minutes 4.70 seconds (2044.70 seconds total)