Starting phenix.real_space_refine on Wed Mar 4 19:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu1_21902/03_2026/6wu1_21902.map" } resolution = 3.09 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5222 2.51 5 N 1176 2.21 5 O 1260 1.98 5 H 7826 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15534 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7673 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "B" Number of atoms: 7673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 7673 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 22, 'TRANS': 466} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 110 Unusual residues: {'D10': 5, 'HEX': 6, 'OCT': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 78 Unusual residues: {'D10': 3, 'HEX': 4, 'OCT': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 2.94, per 1000 atoms: 0.19 Number of scatterers: 15534 At special positions: 0 Unit cell: (78.6, 103.752, 77.552, 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 50 16.00 O 1260 8.00 N 1176 7.00 C 5222 6.00 H 7826 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 433.2 milliseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1784 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 80.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 34 through 54 Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.568A pdb=" N THR A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.613A pdb=" N ARG A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 removed outlier: 4.030A pdb=" N ALA A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 181 through 186 removed outlier: 4.051A pdb=" N LYS A 185 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 206 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.803A pdb=" N LEU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 removed outlier: 5.148A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 280 through 300 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 311 through 325 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 358 removed outlier: 3.954A pdb=" N TRP A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.661A pdb=" N VAL A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.900A pdb=" N MET A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 455 through 485 Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.568A pdb=" N THR B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.613A pdb=" N ARG B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.029A pdb=" N ALA B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 181 through 186 removed outlier: 4.050A pdb=" N LYS B 185 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 186 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 206 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.803A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 255 removed outlier: 5.147A pdb=" N VAL B 238 " --> pdb=" O TRP B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Proline residue: B 248 - end of helix Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 280 through 300 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 335 through 358 removed outlier: 3.954A pdb=" N TRP B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 372 removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 Processing helix chain 'B' and resid 392 through 395 Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.900A pdb=" N MET B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 419 through 434 Processing helix chain 'B' and resid 442 through 449 Processing helix chain 'B' and resid 455 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 540 hydrogen bonds defined for protein. 1590 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: 3.27 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7822 1.03 - 1.22: 4 1.22 - 1.42: 3154 1.42 - 1.61: 4648 1.61 - 1.81: 96 Bond restraints: 15724 Sorted by residual: bond pdb=" N ALA A 0 " pdb=" CA ALA A 0 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.58e+00 bond pdb=" N ALA B 0 " pdb=" CA ALA B 0 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.45e+00 bond pdb=" N ALA B 0 " pdb=" H ALA B 0 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" N ALA A 0 " pdb=" H ALA A 0 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 HEX A 513 " pdb=" C2 HEX A 513 " ideal model delta sigma weight residual 1.523 1.494 0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 15719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.40: 28446 7.40 - 14.79: 1 14.79 - 22.19: 0 22.19 - 29.59: 0 29.59 - 36.99: 3 Bond angle restraints: 28450 Sorted by residual: angle pdb=" C ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 109.00 72.01 36.99 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 110.00 73.68 36.32 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CB ALA B 0 " pdb=" CA ALA B 0 " pdb=" HA ALA B 0 " ideal model delta sigma weight residual 109.00 75.92 33.08 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N THR A 438 " pdb=" CA THR A 438 " pdb=" C THR A 438 " ideal model delta sigma weight residual 108.34 112.90 -4.56 1.31e+00 5.83e-01 1.21e+01 angle pdb=" N THR B 438 " pdb=" CA THR B 438 " pdb=" C THR B 438 " ideal model delta sigma weight residual 108.34 112.84 -4.50 1.31e+00 5.83e-01 1.18e+01 ... (remaining 28445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6340 17.41 - 34.82: 698 34.82 - 52.22: 266 52.22 - 69.63: 90 69.63 - 87.04: 10 Dihedral angle restraints: 7404 sinusoidal: 3964 harmonic: 3440 Sorted by residual: dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N ILE B 58 " pdb=" CA ILE B 58 " ideal model delta harmonic sigma weight residual -180.00 -152.70 -27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ILE A 485 " pdb=" C ILE A 485 " pdb=" N GLY A 486 " pdb=" CA GLY A 486 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 735 0.032 - 0.064: 352 0.064 - 0.097: 116 0.097 - 0.129: 35 0.129 - 0.161: 4 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ALA B 0 " pdb=" N ALA B 0 " pdb=" C ALA B 0 " pdb=" CB ALA B 0 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ALA A 0 " pdb=" N ALA A 0 " pdb=" C ALA A 0 " pdb=" CB ALA A 0 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA ILE A 375 " pdb=" N ILE A 375 " pdb=" C ILE A 375 " pdb=" CB ILE A 375 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1239 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 165 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 166 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 165 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 166 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 181 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.60e+00 pdb=" N PRO A 182 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.018 5.00e-02 4.00e+02 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 171 2.05 - 2.69: 24416 2.69 - 3.33: 46808 3.33 - 3.96: 58846 3.96 - 4.60: 96149 Nonbonded interactions: 226390 Sorted by model distance: nonbonded pdb=" O ARG B 134 " pdb=" H GLY B 137 " model vdw 1.416 2.450 nonbonded pdb=" O ARG A 134 " pdb=" H GLY A 137 " model vdw 1.416 2.450 nonbonded pdb=" H ALA B 0 " pdb=" HA ALA B 0 " model vdw 1.576 1.816 nonbonded pdb=" O GLY B 65 " pdb=" HG1 THR B 69 " model vdw 1.623 2.450 nonbonded pdb=" O GLY A 65 " pdb=" HG1 THR A 69 " model vdw 1.627 2.450 ... (remaining 226385 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' and (resid 0 through 488 or resid 502 or resid 506 through 507)) selection = (chain 'B' and (resid 0 through 488 or resid 502 or resid 506 through 507)) } 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.210 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.007 0.040 7898 Z= 0.275 Angle : 0.780 7.434 10690 Z= 0.380 Chirality : 0.042 0.161 1242 Planarity : 0.004 0.037 1254 Dihedral : 15.684 85.294 2766 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.44 % Favored : 94.15 % Rotamer: Outliers : 2.78 % Allowed : 15.19 % Favored : 82.03 % 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 are not related in a simple way. whole: -2.60 (0.24), residues: 974 helix: -1.26 (0.17), residues: 742 sheet: None (None), residues: 0 loop : -2.73 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.008 0.001 TYR B 252 PHE 0.009 0.001 PHE B 464 TRP 0.017 0.001 TRP B 344 HIS 0.006 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 7898) covalent geometry : angle 0.77974 (10690) hydrogen bonds : bond 0.12241 ( 540) hydrogen bonds : angle 5.86251 ( 1590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.366 Fit side-chains REVERT: A 131 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7300 (p90) REVERT: A 253 LYS cc_start: 0.7526 (tptm) cc_final: 0.7126 (tttm) REVERT: B 131 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 253 LYS cc_start: 0.7911 (tptm) cc_final: 0.7361 (tttm) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.1690 time to fit residues: 23.5283 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122658 restraints weight = 24517.961| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.87 r_work: 0.3356 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7898 Z= 0.128 Angle : 0.546 10.377 10690 Z= 0.292 Chirality : 0.041 0.408 1242 Planarity : 0.005 0.042 1254 Dihedral : 7.975 56.637 1160 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 2.53 % Allowed : 15.44 % Favored : 82.03 % 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 are not related in a simple way. whole: -0.50 (0.27), residues: 974 helix: 0.24 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.98 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 159 TYR 0.011 0.001 TYR A 255 PHE 0.010 0.001 PHE A 474 TRP 0.016 0.001 TRP A 344 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7898) covalent geometry : angle 0.54643 (10690) hydrogen bonds : bond 0.04208 ( 540) hydrogen bonds : angle 4.81860 ( 1590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.380 Fit side-chains REVERT: A 131 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.6999 (p90) REVERT: A 253 LYS cc_start: 0.7819 (tptm) cc_final: 0.7229 (tttm) REVERT: B 131 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7049 (p90) REVERT: B 219 MET cc_start: 0.8169 (mmm) cc_final: 0.7241 (mmt) REVERT: B 253 LYS cc_start: 0.8144 (tptm) cc_final: 0.7405 (tttm) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.1804 time to fit residues: 25.3497 Evaluate side-chains 89 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 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 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129442 restraints weight = 25780.391| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.85 r_work: 0.3439 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7898 Z= 0.116 Angle : 0.508 10.390 10690 Z= 0.270 Chirality : 0.041 0.427 1242 Planarity : 0.005 0.042 1254 Dihedral : 6.932 58.771 1147 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 1.01 % Allowed : 16.71 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.28), residues: 974 helix: 0.92 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -1.68 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 159 TYR 0.011 0.001 TYR A 255 PHE 0.009 0.001 PHE B 474 TRP 0.015 0.001 TRP A 344 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7898) covalent geometry : angle 0.50791 (10690) hydrogen bonds : bond 0.03862 ( 540) hydrogen bonds : angle 4.55307 ( 1590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.353 Fit side-chains REVERT: A 5 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7921 (mt-10) REVERT: A 131 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7067 (p90) REVERT: A 253 LYS cc_start: 0.8046 (tptm) cc_final: 0.7395 (tttm) REVERT: A 462 MET cc_start: 0.8417 (mtm) cc_final: 0.8157 (mtm) REVERT: A 482 MET cc_start: 0.6839 (mtt) cc_final: 0.6323 (mtt) REVERT: B 131 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7088 (p90) REVERT: B 219 MET cc_start: 0.8306 (mmm) cc_final: 0.8076 (mmm) REVERT: B 253 LYS cc_start: 0.8448 (tptm) cc_final: 0.7746 (tttm) outliers start: 8 outliers final: 3 residues processed: 99 average time/residue: 0.1682 time to fit residues: 24.1424 Evaluate side-chains 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 199 ASN A 264 ASN B 121 ASN B 199 ASN B 264 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112697 restraints weight = 27866.479| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.85 r_work: 0.3276 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 7898 Z= 0.256 Angle : 0.627 10.166 10690 Z= 0.343 Chirality : 0.046 0.428 1242 Planarity : 0.006 0.049 1254 Dihedral : 8.363 59.484 1140 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 3.42 % Allowed : 15.95 % Favored : 80.63 % 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 are not related in a simple way. whole: 0.04 (0.27), residues: 974 helix: 0.56 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -1.66 (0.47), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 184 TYR 0.022 0.002 TYR A 255 PHE 0.016 0.002 PHE B 474 TRP 0.020 0.002 TRP B 344 HIS 0.007 0.002 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 7898) covalent geometry : angle 0.62749 (10690) hydrogen bonds : bond 0.04816 ( 540) hydrogen bonds : angle 4.96805 ( 1590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.289 Fit side-chains REVERT: A 131 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6995 (p90) REVERT: A 253 LYS cc_start: 0.8628 (tptm) cc_final: 0.7918 (tttm) REVERT: A 264 ASN cc_start: 0.6281 (OUTLIER) cc_final: 0.6076 (p0) REVERT: B 131 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7096 (p90) REVERT: B 253 LYS cc_start: 0.8642 (tptm) cc_final: 0.7910 (tttm) REVERT: B 264 ASN cc_start: 0.6477 (OUTLIER) cc_final: 0.6263 (p0) outliers start: 27 outliers final: 12 residues processed: 113 average time/residue: 0.1644 time to fit residues: 26.6891 Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114427 restraints weight = 27728.449| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.87 r_work: 0.3300 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7898 Z= 0.170 Angle : 0.556 10.359 10690 Z= 0.301 Chirality : 0.042 0.429 1242 Planarity : 0.006 0.046 1254 Dihedral : 7.640 58.811 1138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 1.90 % Allowed : 17.59 % Favored : 80.51 % 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 are not related in a simple way. whole: 0.34 (0.28), residues: 974 helix: 0.79 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.53 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.007 0.001 TYR A 470 PHE 0.011 0.001 PHE B 474 TRP 0.016 0.001 TRP A 344 HIS 0.006 0.002 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 7898) covalent geometry : angle 0.55650 (10690) hydrogen bonds : bond 0.04225 ( 540) hydrogen bonds : angle 4.79737 ( 1590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.394 Fit side-chains REVERT: A 131 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7005 (p90) REVERT: A 253 LYS cc_start: 0.8669 (tptm) cc_final: 0.7932 (tttm) REVERT: B 131 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7106 (p90) REVERT: B 253 LYS cc_start: 0.8659 (tptm) cc_final: 0.7931 (tttm) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.1717 time to fit residues: 24.5639 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103594 restraints weight = 27379.337| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.05 r_work: 0.3155 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7898 Z= 0.152 Angle : 0.535 10.402 10690 Z= 0.286 Chirality : 0.042 0.430 1242 Planarity : 0.006 0.044 1254 Dihedral : 7.030 58.306 1138 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 1.39 % Allowed : 18.86 % Favored : 79.75 % 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 are not related in a simple way. whole: 0.59 (0.28), residues: 974 helix: 0.97 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -1.44 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.007 0.001 TYR B 255 PHE 0.010 0.001 PHE A 474 TRP 0.015 0.001 TRP A 344 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7898) covalent geometry : angle 0.53528 (10690) hydrogen bonds : bond 0.03931 ( 540) hydrogen bonds : angle 4.65321 ( 1590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.385 Fit side-chains REVERT: A 131 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.6681 (p90) REVERT: A 253 LYS cc_start: 0.8553 (tptm) cc_final: 0.7736 (tttm) REVERT: B 1 MET cc_start: 0.7615 (ttt) cc_final: 0.7339 (ttt) REVERT: B 131 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6753 (p90) REVERT: B 253 LYS cc_start: 0.8577 (tptm) cc_final: 0.7745 (tttm) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.1763 time to fit residues: 23.8780 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 264 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102990 restraints weight = 27532.119| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.05 r_work: 0.3145 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7898 Z= 0.162 Angle : 0.541 10.383 10690 Z= 0.290 Chirality : 0.042 0.430 1242 Planarity : 0.005 0.044 1254 Dihedral : 6.963 58.559 1138 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.93 % Favored : 94.87 % Rotamer: Outliers : 1.90 % Allowed : 19.11 % Favored : 78.99 % 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 are not related in a simple way. whole: 0.70 (0.28), residues: 974 helix: 1.04 (0.19), residues: 754 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.007 0.001 TYR B 390 PHE 0.010 0.001 PHE B 474 TRP 0.015 0.001 TRP B 344 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7898) covalent geometry : angle 0.54067 (10690) hydrogen bonds : bond 0.03953 ( 540) hydrogen bonds : angle 4.65640 ( 1590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.395 Fit side-chains REVERT: A 131 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6752 (p90) REVERT: A 253 LYS cc_start: 0.8567 (tptm) cc_final: 0.7751 (tttm) REVERT: B 1 MET cc_start: 0.7692 (ttt) cc_final: 0.7408 (ttt) REVERT: B 131 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.6785 (p90) REVERT: B 253 LYS cc_start: 0.8587 (tptm) cc_final: 0.7759 (tttm) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.1906 time to fit residues: 27.0855 Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS B 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105160 restraints weight = 27620.572| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.09 r_work: 0.3133 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7898 Z= 0.179 Angle : 0.552 10.349 10690 Z= 0.295 Chirality : 0.042 0.430 1242 Planarity : 0.006 0.044 1254 Dihedral : 7.002 59.370 1138 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.16 % Favored : 93.63 % Rotamer: Outliers : 2.41 % Allowed : 18.61 % Favored : 78.99 % 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 are not related in a simple way. whole: 0.66 (0.28), residues: 974 helix: 1.02 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.46 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 159 TYR 0.008 0.001 TYR B 390 PHE 0.010 0.001 PHE B 474 TRP 0.016 0.001 TRP A 344 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7898) covalent geometry : angle 0.55152 (10690) hydrogen bonds : bond 0.04042 ( 540) hydrogen bonds : angle 4.66171 ( 1590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.394 Fit side-chains REVERT: A 131 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6679 (p90) REVERT: A 134 ARG cc_start: 0.6690 (mtp180) cc_final: 0.6343 (mmt-90) REVERT: A 253 LYS cc_start: 0.8589 (tptm) cc_final: 0.7758 (tttm) REVERT: B 131 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6773 (p90) REVERT: B 253 LYS cc_start: 0.8569 (tptm) cc_final: 0.7760 (tttm) outliers start: 19 outliers final: 14 residues processed: 105 average time/residue: 0.1867 time to fit residues: 27.5355 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.115865 restraints weight = 27825.940| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.87 r_work: 0.3323 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7898 Z= 0.124 Angle : 0.519 10.416 10690 Z= 0.276 Chirality : 0.041 0.430 1242 Planarity : 0.005 0.042 1254 Dihedral : 6.653 59.839 1138 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.72 % Favored : 95.07 % Rotamer: Outliers : 1.27 % Allowed : 20.00 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 974 helix: 1.23 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.41 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.006 0.001 TYR B 390 PHE 0.009 0.001 PHE B 474 TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7898) covalent geometry : angle 0.51905 (10690) hydrogen bonds : bond 0.03692 ( 540) hydrogen bonds : angle 4.53892 ( 1590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.342 Fit side-chains REVERT: A 131 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6833 (p90) REVERT: A 219 MET cc_start: 0.8404 (mmm) cc_final: 0.7829 (mmt) REVERT: A 253 LYS cc_start: 0.8676 (tptm) cc_final: 0.7935 (tttm) REVERT: B 131 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6882 (p90) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.1824 time to fit residues: 25.7232 Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118685 restraints weight = 27725.410| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.88 r_work: 0.3300 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7898 Z= 0.162 Angle : 0.540 10.408 10690 Z= 0.288 Chirality : 0.042 0.431 1242 Planarity : 0.005 0.043 1254 Dihedral : 6.712 59.858 1138 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 1.27 % Allowed : 20.38 % Favored : 78.35 % 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 are not related in a simple way. whole: 0.88 (0.28), residues: 974 helix: 1.18 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.008 0.001 TYR A 470 PHE 0.010 0.001 PHE B 474 TRP 0.015 0.001 TRP A 344 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7898) covalent geometry : angle 0.54033 (10690) hydrogen bonds : bond 0.03892 ( 540) hydrogen bonds : angle 4.59277 ( 1590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.383 Fit side-chains REVERT: A 131 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.6846 (p90) REVERT: A 134 ARG cc_start: 0.6955 (mtp180) cc_final: 0.6679 (mmt-90) REVERT: A 219 MET cc_start: 0.8438 (mmm) cc_final: 0.7790 (mmt) REVERT: A 253 LYS cc_start: 0.8690 (tptm) cc_final: 0.7943 (tttm) REVERT: B 38 TRP cc_start: 0.8549 (t-100) cc_final: 0.8347 (t-100) REVERT: B 131 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.6890 (p90) REVERT: B 219 MET cc_start: 0.8466 (mmm) cc_final: 0.7911 (mmt) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.2101 time to fit residues: 26.9214 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 487 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116080 restraints weight = 27073.862| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.80 r_work: 0.3330 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7898 Z= 0.120 Angle : 0.516 10.431 10690 Z= 0.274 Chirality : 0.041 0.431 1242 Planarity : 0.005 0.042 1254 Dihedral : 6.437 59.402 1138 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.93 % Favored : 94.87 % Rotamer: Outliers : 1.27 % Allowed : 20.13 % Favored : 78.61 % 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 are not related in a simple way. whole: 1.04 (0.28), residues: 974 helix: 1.31 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -1.36 (0.47), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 159 TYR 0.006 0.001 TYR A 470 PHE 0.008 0.001 PHE A 474 TRP 0.013 0.001 TRP B 344 HIS 0.004 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7898) covalent geometry : angle 0.51616 (10690) hydrogen bonds : bond 0.03630 ( 540) hydrogen bonds : angle 4.49451 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.10 seconds wall clock time: 58 minutes 26.63 seconds (3506.63 seconds total)