Starting phenix.real_space_refine on Tue Feb 3 20:43:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u84_63951/02_2026/9u84_63951.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4422 2.51 5 N 1098 2.21 5 O 1152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6708 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3354 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Chain: "B" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3354 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 19, 'TRANS': 428} Time building chain proxies: 1.68, per 1000 atoms: 0.25 Number of scatterers: 6708 At special positions: 0 Unit cell: (75.2, 73.696, 107.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1152 8.00 N 1098 7.00 C 4422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 275.6 milliseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 82.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 removed outlier: 3.997A pdb=" N GLY A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 32 through 73 Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.750A pdb=" N GLY A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 122 through 125 removed outlier: 3.697A pdb=" N ASN A 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 142 through 164 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.509A pdb=" N THR A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 4.151A pdb=" N TYR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.647A pdb=" N ALA A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 239 Processing helix chain 'A' and resid 242 through 286 Proline residue: A 261 - end of helix Proline residue: A 266 - end of helix Proline residue: A 273 - end of helix removed outlier: 4.203A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.659A pdb=" N GLY A 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 324 removed outlier: 3.532A pdb=" N VAL A 307 " --> pdb=" O HIS A 303 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix removed outlier: 3.709A pdb=" N VAL A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.079A pdb=" N VAL A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N MET A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 417 through 448 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 32 through 73 Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.668A pdb=" N GLY B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 4.437A pdb=" N ILE B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 142 through 164 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 181 through 187 removed outlier: 4.075A pdb=" N ALA B 185 " --> pdb=" O HIS B 181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.739A pdb=" N ALA B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 223 through 239 Processing helix chain 'B' and resid 242 through 286 Proline residue: B 261 - end of helix Proline residue: B 266 - end of helix Proline residue: B 273 - end of helix removed outlier: 4.117A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.543A pdb=" N LEU B 299 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 324 removed outlier: 3.894A pdb=" N ILE B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix removed outlier: 3.763A pdb=" N VAL B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 removed outlier: 4.048A pdb=" N VAL B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET B 344 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 374 Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 417 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 79 removed outlier: 7.076A pdb=" N VAL A 78 " --> pdb=" O LEU A 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 330 removed outlier: 5.648A pdb=" N VAL B 79 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 120 505 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2096 1.34 - 1.46: 1537 1.46 - 1.58: 3145 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6850 Sorted by residual: bond pdb=" CG1 ILE A 45 " pdb=" CD1 ILE A 45 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.15e+00 bond pdb=" CG1 ILE B 370 " pdb=" CD1 ILE B 370 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" CB ASP B 399 " pdb=" CG ASP B 399 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.57e-01 bond pdb=" CB VAL A 256 " pdb=" CG2 VAL A 256 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.13e-01 bond pdb=" CA MET A 260 " pdb=" C MET A 260 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.20e-01 ... (remaining 6845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 9241 2.36 - 4.73: 71 4.73 - 7.09: 18 7.09 - 9.45: 0 9.45 - 11.81: 2 Bond angle restraints: 9332 Sorted by residual: angle pdb=" CB MET B 17 " pdb=" CG MET B 17 " pdb=" SD MET B 17 " ideal model delta sigma weight residual 112.70 124.51 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ILE B 95 " pdb=" CA ILE B 95 " pdb=" C ILE B 95 " ideal model delta sigma weight residual 111.91 108.56 3.35 8.90e-01 1.26e+00 1.42e+01 angle pdb=" N ILE B 98 " pdb=" CA ILE B 98 " pdb=" C ILE B 98 " ideal model delta sigma weight residual 113.39 108.01 5.38 1.47e+00 4.63e-01 1.34e+01 angle pdb=" CB MET B 260 " pdb=" CG MET B 260 " pdb=" SD MET B 260 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CA ILE B 98 " pdb=" C ILE B 98 " pdb=" N ALA B 99 " ideal model delta sigma weight residual 118.55 115.90 2.65 8.60e-01 1.35e+00 9.52e+00 ... (remaining 9327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3385 14.86 - 29.72: 417 29.72 - 44.58: 139 44.58 - 59.44: 43 59.44 - 74.30: 14 Dihedral angle restraints: 3998 sinusoidal: 1482 harmonic: 2516 Sorted by residual: dihedral pdb=" CA ASP A 212 " pdb=" CB ASP A 212 " pdb=" CG ASP A 212 " pdb=" OD1 ASP A 212 " ideal model delta sinusoidal sigma weight residual -30.00 -83.94 53.94 1 2.00e+01 2.50e-03 9.87e+00 dihedral pdb=" CA GLU A 223 " pdb=" C GLU A 223 " pdb=" N PRO A 224 " pdb=" CA PRO A 224 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CB MET A 110 " pdb=" CG MET A 110 " pdb=" SD MET A 110 " pdb=" CE MET A 110 " ideal model delta sinusoidal sigma weight residual 60.00 2.28 57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 917 0.052 - 0.103: 217 0.103 - 0.155: 16 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CG LEU B 311 " pdb=" CB LEU B 311 " pdb=" CD1 LEU B 311 " pdb=" CD2 LEU B 311 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 45 " pdb=" N ILE A 45 " pdb=" C ILE A 45 " pdb=" CB ILE A 45 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA TRP A 83 " pdb=" N TRP A 83 " pdb=" C TRP A 83 " pdb=" CB TRP A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1149 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 188 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO B 189 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 189 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 189 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 188 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 189 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 18 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO B 19 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 19 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 19 " -0.019 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 247 2.72 - 3.27: 7110 3.27 - 3.81: 11759 3.81 - 4.36: 12780 4.36 - 4.90: 23157 Nonbonded interactions: 55053 Sorted by model distance: nonbonded pdb=" O TYR B 186 " pdb=" OH TYR B 428 " model vdw 2.179 3.040 nonbonded pdb=" O TYR A 186 " pdb=" OH TYR A 428 " model vdw 2.182 3.040 nonbonded pdb=" NE2 HIS A 349 " pdb=" OG SER A 359 " model vdw 2.265 3.120 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.297 3.120 nonbonded pdb=" O LEU A 56 " pdb=" OG SER A 60 " model vdw 2.315 3.040 ... (remaining 55048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.003 0.069 6850 Z= 0.121 Angle : 0.554 11.813 9332 Z= 0.282 Chirality : 0.040 0.259 1152 Planarity : 0.003 0.040 1146 Dihedral : 15.952 74.299 2390 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.98 % Allowed : 24.93 % Favored : 73.09 % 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: 2.52 (0.29), residues: 892 helix: 2.26 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.36 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 355 TYR 0.012 0.001 TYR A 186 PHE 0.010 0.001 PHE A 47 TRP 0.007 0.001 TRP B 127 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6850) covalent geometry : angle 0.55369 ( 9332) hydrogen bonds : bond 0.11936 ( 505) hydrogen bonds : angle 4.93948 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.226 Fit side-chains REVERT: A 37 PHE cc_start: 0.8833 (t80) cc_final: 0.8546 (t80) outliers start: 14 outliers final: 14 residues processed: 91 average time/residue: 0.0558 time to fit residues: 7.7860 Evaluate side-chains 94 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 311 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.063263 restraints weight = 17813.050| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.96 r_work: 0.2786 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6850 Z= 0.136 Angle : 0.513 6.210 9332 Z= 0.265 Chirality : 0.041 0.145 1152 Planarity : 0.004 0.042 1146 Dihedral : 5.278 49.914 958 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.12 % Allowed : 21.95 % Favored : 74.93 % 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: 2.53 (0.29), residues: 892 helix: 2.31 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.60 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 206 TYR 0.012 0.001 TYR A 186 PHE 0.010 0.001 PHE A 47 TRP 0.008 0.001 TRP B 127 HIS 0.004 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6850) covalent geometry : angle 0.51348 ( 9332) hydrogen bonds : bond 0.03918 ( 505) hydrogen bonds : angle 4.14352 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.217 Fit side-chains REVERT: A 27 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 400 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8095 (tp-100) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 0.0543 time to fit residues: 7.9217 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.080179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063916 restraints weight = 18242.686| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.60 r_work: 0.2903 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6850 Z= 0.122 Angle : 0.495 5.920 9332 Z= 0.254 Chirality : 0.040 0.146 1152 Planarity : 0.004 0.042 1146 Dihedral : 4.253 43.302 940 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.26 % Allowed : 22.24 % Favored : 74.50 % 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: 2.49 (0.29), residues: 892 helix: 2.28 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.64 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.011 0.001 TYR A 186 PHE 0.016 0.001 PHE A 47 TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6850) covalent geometry : angle 0.49522 ( 9332) hydrogen bonds : bond 0.03598 ( 505) hydrogen bonds : angle 3.95282 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.217 Fit side-chains REVERT: B 17 MET cc_start: 0.8183 (tpt) cc_final: 0.7804 (tpp) REVERT: B 31 MET cc_start: 0.8942 (mtt) cc_final: 0.8694 (mtt) REVERT: B 400 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8328 (tp-100) outliers start: 23 outliers final: 9 residues processed: 94 average time/residue: 0.0543 time to fit residues: 7.6855 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.080181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063885 restraints weight = 18242.783| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.59 r_work: 0.2904 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6850 Z= 0.126 Angle : 0.492 5.913 9332 Z= 0.251 Chirality : 0.040 0.152 1152 Planarity : 0.004 0.043 1146 Dihedral : 4.152 41.393 939 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.69 % Allowed : 23.51 % Favored : 73.80 % 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: 2.47 (0.29), residues: 892 helix: 2.26 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.64 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 355 TYR 0.011 0.001 TYR A 186 PHE 0.014 0.001 PHE A 47 TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6850) covalent geometry : angle 0.49216 ( 9332) hydrogen bonds : bond 0.03541 ( 505) hydrogen bonds : angle 3.91998 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.261 Fit side-chains REVERT: B 17 MET cc_start: 0.8179 (tpt) cc_final: 0.7816 (tpp) REVERT: B 400 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8352 (tp-100) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.0596 time to fit residues: 8.2396 Evaluate side-chains 81 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.0170 chunk 75 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.080373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064144 restraints weight = 18446.164| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.61 r_work: 0.2907 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6850 Z= 0.120 Angle : 0.496 6.427 9332 Z= 0.253 Chirality : 0.040 0.153 1152 Planarity : 0.004 0.043 1146 Dihedral : 4.118 39.238 939 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.97 % Allowed : 23.94 % Favored : 73.09 % 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: 2.48 (0.29), residues: 892 helix: 2.27 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.63 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 438 TYR 0.011 0.001 TYR A 186 PHE 0.013 0.001 PHE A 47 TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6850) covalent geometry : angle 0.49649 ( 9332) hydrogen bonds : bond 0.03485 ( 505) hydrogen bonds : angle 3.85241 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.231 Fit side-chains REVERT: B 17 MET cc_start: 0.8094 (tpt) cc_final: 0.7706 (tpp) REVERT: B 400 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8412 (tp-100) outliers start: 21 outliers final: 10 residues processed: 95 average time/residue: 0.0500 time to fit residues: 7.2499 Evaluate side-chains 82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.079726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.063603 restraints weight = 18460.685| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.59 r_work: 0.2899 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6850 Z= 0.133 Angle : 0.518 6.184 9332 Z= 0.262 Chirality : 0.041 0.157 1152 Planarity : 0.004 0.044 1146 Dihedral : 3.833 35.213 937 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.97 % Allowed : 23.51 % Favored : 73.51 % 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: 2.42 (0.29), residues: 892 helix: 2.21 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 438 TYR 0.011 0.001 TYR A 186 PHE 0.012 0.001 PHE A 47 TRP 0.009 0.001 TRP B 124 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6850) covalent geometry : angle 0.51843 ( 9332) hydrogen bonds : bond 0.03564 ( 505) hydrogen bonds : angle 3.83796 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.262 Fit side-chains REVERT: B 17 MET cc_start: 0.8135 (tpt) cc_final: 0.7750 (tpp) REVERT: B 31 MET cc_start: 0.8936 (mtt) cc_final: 0.8720 (mtt) REVERT: B 400 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8336 (tp-100) outliers start: 21 outliers final: 13 residues processed: 88 average time/residue: 0.0703 time to fit residues: 9.0421 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.080376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064291 restraints weight = 18180.521| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.55 r_work: 0.2915 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6850 Z= 0.119 Angle : 0.517 8.686 9332 Z= 0.261 Chirality : 0.040 0.156 1152 Planarity : 0.004 0.042 1146 Dihedral : 3.791 36.405 937 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.97 % Allowed : 23.80 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.29), residues: 892 helix: 2.23 (0.20), residues: 694 sheet: -2.54 (1.89), residues: 10 loop : -0.49 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 114 TYR 0.012 0.001 TYR A 186 PHE 0.011 0.001 PHE A 47 TRP 0.009 0.001 TRP B 127 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6850) covalent geometry : angle 0.51665 ( 9332) hydrogen bonds : bond 0.03462 ( 505) hydrogen bonds : angle 3.82180 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.238 Fit side-chains REVERT: B 17 MET cc_start: 0.8120 (tpt) cc_final: 0.7744 (tpp) REVERT: B 400 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8418 (tp-100) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.0528 time to fit residues: 7.3265 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 400 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.079806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.063687 restraints weight = 18345.259| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.58 r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6850 Z= 0.133 Angle : 0.539 9.095 9332 Z= 0.269 Chirality : 0.041 0.158 1152 Planarity : 0.004 0.043 1146 Dihedral : 3.763 36.761 937 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.69 % Allowed : 23.94 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.41 (0.29), residues: 892 helix: 2.21 (0.20), residues: 694 sheet: -2.57 (1.89), residues: 10 loop : -0.47 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.011 0.001 TYR A 186 PHE 0.012 0.001 PHE A 47 TRP 0.008 0.001 TRP B 124 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6850) covalent geometry : angle 0.53923 ( 9332) hydrogen bonds : bond 0.03581 ( 505) hydrogen bonds : angle 3.82907 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.269 Fit side-chains REVERT: B 17 MET cc_start: 0.8148 (tpt) cc_final: 0.7780 (tpp) outliers start: 19 outliers final: 15 residues processed: 87 average time/residue: 0.0578 time to fit residues: 7.8109 Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.0070 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.080075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.063895 restraints weight = 18370.690| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.61 r_work: 0.2908 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6850 Z= 0.126 Angle : 0.558 9.702 9332 Z= 0.273 Chirality : 0.041 0.159 1152 Planarity : 0.004 0.043 1146 Dihedral : 3.510 28.809 935 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.69 % Allowed : 24.22 % Favored : 73.09 % 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: 2.44 (0.29), residues: 892 helix: 2.23 (0.20), residues: 692 sheet: -2.49 (1.92), residues: 10 loop : -0.46 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 355 TYR 0.012 0.001 TYR A 186 PHE 0.013 0.001 PHE A 47 TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6850) covalent geometry : angle 0.55765 ( 9332) hydrogen bonds : bond 0.03509 ( 505) hydrogen bonds : angle 3.80957 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.217 Fit side-chains REVERT: B 17 MET cc_start: 0.8152 (tpt) cc_final: 0.7791 (tpp) REVERT: B 31 MET cc_start: 0.8987 (mtt) cc_final: 0.8229 (mtt) outliers start: 19 outliers final: 15 residues processed: 83 average time/residue: 0.0613 time to fit residues: 7.7696 Evaluate side-chains 84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063821 restraints weight = 18181.940| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.55 r_work: 0.2912 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 6850 Z= 0.125 Angle : 0.563 10.130 9332 Z= 0.276 Chirality : 0.041 0.213 1152 Planarity : 0.004 0.043 1146 Dihedral : 3.516 28.780 935 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 24.22 % Favored : 73.51 % 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: 2.44 (0.29), residues: 892 helix: 2.23 (0.20), residues: 692 sheet: -2.71 (1.82), residues: 10 loop : -0.44 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.012 0.001 TYR A 186 PHE 0.013 0.001 PHE A 37 TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6850) covalent geometry : angle 0.56308 ( 9332) hydrogen bonds : bond 0.03499 ( 505) hydrogen bonds : angle 3.79026 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.235 Fit side-chains REVERT: B 17 MET cc_start: 0.8154 (tpt) cc_final: 0.7800 (tpp) REVERT: B 31 MET cc_start: 0.8976 (mtt) cc_final: 0.8224 (mtt) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0562 time to fit residues: 7.0511 Evaluate side-chains 83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain B residue 72 PHE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 356 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.079574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063511 restraints weight = 18176.947| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.55 r_work: 0.2905 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6850 Z= 0.128 Angle : 0.562 10.072 9332 Z= 0.275 Chirality : 0.042 0.239 1152 Planarity : 0.004 0.043 1146 Dihedral : 3.513 28.903 935 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.27 % Allowed : 23.94 % Favored : 73.80 % 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: 2.43 (0.29), residues: 892 helix: 2.23 (0.20), residues: 692 sheet: -2.98 (1.68), residues: 10 loop : -0.44 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.012 0.001 TYR A 186 PHE 0.013 0.001 PHE A 47 TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6850) covalent geometry : angle 0.56168 ( 9332) hydrogen bonds : bond 0.03517 ( 505) hydrogen bonds : angle 3.77678 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1489.29 seconds wall clock time: 26 minutes 21.08 seconds (1581.08 seconds total)