Starting phenix.real_space_refine on Tue Mar 3 19:03:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2026/6wut_21918.map" } resolution = 3.0 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= 0.004 sd= 0.147 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 16 5.16 5 C 5217 2.51 5 N 1463 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 8218 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2295 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 22, 'TRANS': 273} Chain breaks: 2 Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "C" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2628 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 25, 'TRANS': 322} Chain breaks: 3 Time building chain proxies: 1.78, per 1000 atoms: 0.22 Number of scatterers: 8218 At special positions: 0 Unit cell: (93.28, 127.2, 113.42, 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 16 16.00 O 1522 8.00 N 1463 7.00 C 5217 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: 0.66 Conformation dependent library (CDL) restraints added in 290.1 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 38.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.312A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.688A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 213 Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.642A pdb=" N GLY A 233 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 234 " --> pdb=" O ALA A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 234' Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.585A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.545A pdb=" N THR A 265 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.070A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.550A pdb=" N GLU A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.976A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.586A pdb=" N ASP B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.958A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 123 Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.590A pdb=" N LEU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.649A pdb=" N GLY C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.589A pdb=" N ALA C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.797A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 4.169A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.693A pdb=" N ARG C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.666A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 removed outlier: 3.804A pdb=" N GLY C 319 " --> pdb=" O PRO C 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 316 through 319' Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.764A pdb=" N GLY C 327 " --> pdb=" O TRP C 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 357 through 378 Processing helix chain 'C' and resid 386 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.994A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.754A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.146A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 51 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 418 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 142 removed outlier: 3.746A pdb=" N VAL B 171 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR B 179 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 209 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 181 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 198 through 210 Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 240 removed outlier: 4.501A pdb=" N LEU B 290 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 318 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 240 removed outlier: 4.501A pdb=" N LEU B 290 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 318 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 338 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA9, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 41 419 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 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: 1.22 - 1.34: 2574 1.34 - 1.46: 1560 1.46 - 1.58: 4247 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 8408 Sorted by residual: bond pdb=" CB TRP B 244 " pdb=" CG TRP B 244 " ideal model delta sigma weight residual 1.498 1.562 -0.064 3.10e-02 1.04e+03 4.27e+00 bond pdb=" C LEU C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.30e+00 bond pdb=" CG LEU C 52 " pdb=" CD2 LEU C 52 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.413 0.079 5.00e-02 4.00e+02 2.47e+00 bond pdb=" CB PRO C 155 " pdb=" CG PRO C 155 " ideal model delta sigma weight residual 1.492 1.418 0.074 5.00e-02 4.00e+02 2.20e+00 ... (remaining 8403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11059 2.08 - 4.16: 315 4.16 - 6.24: 51 6.24 - 8.32: 9 8.32 - 10.40: 4 Bond angle restraints: 11438 Sorted by residual: angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 120.21 -10.40 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N PHE A 27 " pdb=" CA PHE A 27 " pdb=" C PHE A 27 " ideal model delta sigma weight residual 109.81 119.99 -10.18 2.21e+00 2.05e-01 2.12e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 113.57 119.01 -5.44 1.38e+00 5.25e-01 1.56e+01 angle pdb=" N LEU C 52 " pdb=" CA LEU C 52 " pdb=" C LEU C 52 " ideal model delta sigma weight residual 109.81 118.36 -8.55 2.21e+00 2.05e-01 1.50e+01 angle pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 ... (remaining 11433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4546 17.11 - 34.23: 333 34.23 - 51.34: 80 51.34 - 68.45: 27 68.45 - 85.57: 5 Dihedral angle restraints: 4991 sinusoidal: 1911 harmonic: 3080 Sorted by residual: dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -147.42 -32.58 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA PRO C 151 " pdb=" C PRO C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -148.39 -31.61 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 4988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1037 0.061 - 0.123: 212 0.123 - 0.184: 31 0.184 - 0.245: 2 0.245 - 0.306: 3 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA PHE A 27 " pdb=" N PHE A 27 " pdb=" C PHE A 27 " pdb=" CB PHE A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1282 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 284 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO C 285 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO C 160 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 188 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 189 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.039 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1806 2.78 - 3.31: 6664 3.31 - 3.84: 13102 3.84 - 4.37: 15538 4.37 - 4.90: 27663 Nonbonded interactions: 64773 Sorted by model distance: nonbonded pdb=" OG1 THR B 257 " pdb=" OD2 ASP B 386 " model vdw 2.253 3.040 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 45 " model vdw 2.279 3.040 nonbonded pdb=" O HIS C 51 " pdb=" OG1 THR C 54 " model vdw 2.282 3.040 nonbonded pdb=" O PHE A 55 " pdb=" OG SER A 67 " model vdw 2.300 3.040 nonbonded pdb=" OE2 GLU C 20 " pdb=" OH TYR C 278 " model vdw 2.307 3.040 ... (remaining 64768 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.790 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.750 Find NCS groups from input model: 0.040 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:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.008 0.079 8408 Z= 0.315 Angle : 0.887 10.405 11438 Z= 0.494 Chirality : 0.053 0.306 1285 Planarity : 0.009 0.072 1485 Dihedral : 13.929 85.566 3015 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.79 % Allowed : 9.10 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.07 (0.20), residues: 1065 helix: -2.36 (0.19), residues: 387 sheet: -2.50 (0.31), residues: 234 loop : -2.97 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.016 0.003 TYR A 331 PHE 0.036 0.003 PHE B 396 TRP 0.018 0.003 TRP C 360 HIS 0.009 0.002 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 8408) covalent geometry : angle 0.88745 (11438) hydrogen bonds : bond 0.20387 ( 380) hydrogen bonds : angle 8.56903 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.229 Fit side-chains REVERT: A 206 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: A 312 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: B 108 PHE cc_start: 0.6868 (m-80) cc_final: 0.6612 (m-80) REVERT: B 129 SER cc_start: 0.8358 (t) cc_final: 0.7843 (p) REVERT: B 134 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 155 THR cc_start: 0.8058 (m) cc_final: 0.7825 (p) REVERT: B 167 GLU cc_start: 0.7726 (pt0) cc_final: 0.7361 (pt0) REVERT: B 179 THR cc_start: 0.7843 (p) cc_final: 0.7542 (t) REVERT: B 183 TYR cc_start: 0.7702 (m-80) cc_final: 0.7360 (m-80) REVERT: B 205 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7275 (tpt170) REVERT: B 283 MET cc_start: 0.7894 (mmt) cc_final: 0.7664 (mmp) REVERT: B 378 LYS cc_start: 0.8522 (ttpp) cc_final: 0.7766 (ttpt) REVERT: B 463 ASN cc_start: 0.7928 (t0) cc_final: 0.7381 (p0) REVERT: B 486 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (p0) REVERT: B 494 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8453 (mpt180) REVERT: B 498 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5902 (mt-10) REVERT: C 281 LEU cc_start: 0.8359 (mt) cc_final: 0.8154 (mm) REVERT: C 299 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6799 (mmt90) REVERT: C 356 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 371 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6527 (mtm110) REVERT: C 372 GLU cc_start: 0.7592 (pt0) cc_final: 0.7388 (pt0) outliers start: 49 outliers final: 19 residues processed: 172 average time/residue: 0.5650 time to fit residues: 102.9279 Evaluate side-chains 129 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 69 ASN A 83 ASN A 166 ASN A 178 HIS A 202 HIS A 203 GLN A 310 ASN B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.149576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.120142 restraints weight = 8870.858| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.49 r_work: 0.3048 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8408 Z= 0.175 Angle : 0.636 8.246 11438 Z= 0.322 Chirality : 0.043 0.198 1285 Planarity : 0.007 0.055 1485 Dihedral : 8.279 58.475 1229 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.49 % Allowed : 13.95 % Favored : 81.56 % 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: -2.22 (0.24), residues: 1065 helix: -0.35 (0.25), residues: 402 sheet: -1.71 (0.34), residues: 227 loop : -2.34 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 375 TYR 0.017 0.002 TYR A 53 PHE 0.022 0.002 PHE A 27 TRP 0.016 0.002 TRP C 360 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8408) covalent geometry : angle 0.63616 (11438) hydrogen bonds : bond 0.04416 ( 380) hydrogen bonds : angle 4.93018 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.242 Fit side-chains REVERT: A 206 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8297 (ttp-110) REVERT: B 62 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8665 (pt) REVERT: B 134 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8044 (mt-10) REVERT: B 137 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7624 (mtp-110) REVERT: B 155 THR cc_start: 0.8156 (m) cc_final: 0.7846 (p) REVERT: B 167 GLU cc_start: 0.8397 (pt0) cc_final: 0.8104 (pt0) REVERT: B 179 THR cc_start: 0.7710 (p) cc_final: 0.7376 (t) REVERT: B 205 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7524 (tpt170) REVERT: B 248 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8633 (p) REVERT: B 283 MET cc_start: 0.7930 (mmt) cc_final: 0.7700 (mmp) REVERT: B 463 ASN cc_start: 0.8058 (t0) cc_final: 0.7230 (p0) REVERT: B 498 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6369 (mt-10) REVERT: C 299 ARG cc_start: 0.7845 (mtp85) cc_final: 0.6792 (mmt90) REVERT: C 371 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6717 (mtm110) outliers start: 38 outliers final: 17 residues processed: 137 average time/residue: 0.5946 time to fit residues: 86.1584 Evaluate side-chains 117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 209 GLN B 402 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.152346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125636 restraints weight = 8766.490| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.59 r_work: 0.3082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8408 Z= 0.127 Angle : 0.565 9.003 11438 Z= 0.284 Chirality : 0.041 0.171 1285 Planarity : 0.005 0.044 1485 Dihedral : 6.584 58.551 1205 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.55 % Allowed : 15.72 % Favored : 80.73 % 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: -1.32 (0.25), residues: 1065 helix: 0.63 (0.27), residues: 398 sheet: -1.20 (0.35), residues: 224 loop : -2.10 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 375 TYR 0.016 0.001 TYR A 53 PHE 0.018 0.001 PHE A 27 TRP 0.013 0.001 TRP C 360 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8408) covalent geometry : angle 0.56495 (11438) hydrogen bonds : bond 0.03639 ( 380) hydrogen bonds : angle 4.46832 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.295 Fit side-chains REVERT: A 206 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8403 (ttp-110) REVERT: A 229 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7939 (p0) REVERT: B 50 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7476 (pt0) REVERT: B 155 THR cc_start: 0.8075 (m) cc_final: 0.7857 (p) REVERT: B 167 GLU cc_start: 0.8426 (pt0) cc_final: 0.8171 (pt0) REVERT: B 179 THR cc_start: 0.7889 (p) cc_final: 0.7603 (t) REVERT: B 205 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7612 (tpt170) REVERT: B 283 MET cc_start: 0.7999 (mmt) cc_final: 0.7767 (mmp) REVERT: B 463 ASN cc_start: 0.8014 (t0) cc_final: 0.7193 (p0) REVERT: B 498 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6442 (mt-10) REVERT: C 299 ARG cc_start: 0.7896 (mtp85) cc_final: 0.6901 (mmt90) REVERT: C 371 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6888 (mtm110) outliers start: 30 outliers final: 16 residues processed: 119 average time/residue: 0.5975 time to fit residues: 75.2338 Evaluate side-chains 108 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 358 GLN B 486 ASN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.146450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.114682 restraints weight = 8995.405| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.67 r_work: 0.3064 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8408 Z= 0.198 Angle : 0.624 10.068 11438 Z= 0.313 Chirality : 0.044 0.200 1285 Planarity : 0.006 0.042 1485 Dihedral : 6.477 56.674 1196 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.02 % Allowed : 16.08 % Favored : 79.91 % 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: -1.17 (0.25), residues: 1065 helix: 0.79 (0.27), residues: 398 sheet: -1.19 (0.34), residues: 232 loop : -2.01 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 241 TYR 0.018 0.002 TYR A 53 PHE 0.018 0.002 PHE A 27 TRP 0.012 0.002 TRP C 360 HIS 0.005 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 8408) covalent geometry : angle 0.62397 (11438) hydrogen bonds : bond 0.04331 ( 380) hydrogen bonds : angle 4.46159 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.312 Fit side-chains REVERT: A 267 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7648 (mtp180) REVERT: B 50 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7424 (pt0) REVERT: B 134 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 155 THR cc_start: 0.8100 (m) cc_final: 0.7855 (p) REVERT: B 167 GLU cc_start: 0.8507 (pt0) cc_final: 0.8221 (pt0) REVERT: B 179 THR cc_start: 0.7834 (p) cc_final: 0.7549 (t) REVERT: B 205 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7411 (tpt170) REVERT: B 283 MET cc_start: 0.7919 (mmt) cc_final: 0.7666 (mmp) REVERT: B 463 ASN cc_start: 0.7979 (t0) cc_final: 0.6998 (p0) REVERT: B 498 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6426 (mt-10) REVERT: C -24 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7333 (mt-10) REVERT: C 20 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8345 (mt-10) REVERT: C 244 GLU cc_start: 0.7256 (tp30) cc_final: 0.6795 (mm-30) REVERT: C 299 ARG cc_start: 0.7801 (mtp85) cc_final: 0.6811 (mmt90) REVERT: C 371 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6641 (mtm110) REVERT: C 415 GLU cc_start: 0.7149 (mp0) cc_final: 0.6539 (tt0) outliers start: 34 outliers final: 18 residues processed: 130 average time/residue: 0.6279 time to fit residues: 86.0170 Evaluate side-chains 121 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.148820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.116559 restraints weight = 8809.036| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.72 r_work: 0.3048 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8408 Z= 0.121 Angle : 0.556 10.629 11438 Z= 0.275 Chirality : 0.041 0.166 1285 Planarity : 0.005 0.040 1485 Dihedral : 6.079 54.532 1196 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.26 % Allowed : 15.96 % Favored : 79.79 % 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 (0.26), residues: 1065 helix: 1.22 (0.27), residues: 399 sheet: -0.91 (0.35), residues: 233 loop : -1.80 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.014 0.001 TYR A 53 PHE 0.014 0.001 PHE B 396 TRP 0.013 0.001 TRP C 360 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8408) covalent geometry : angle 0.55570 (11438) hydrogen bonds : bond 0.03389 ( 380) hydrogen bonds : angle 4.23614 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8649 (mtp-110) cc_final: 0.8306 (mtp180) REVERT: A 312 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7268 (mt-10) REVERT: B 50 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7404 (pt0) REVERT: B 134 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 155 THR cc_start: 0.8097 (m) cc_final: 0.7822 (p) REVERT: B 167 GLU cc_start: 0.8476 (pt0) cc_final: 0.8185 (pt0) REVERT: B 179 THR cc_start: 0.7574 (p) cc_final: 0.7373 (t) REVERT: B 205 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7290 (tpt170) REVERT: B 283 MET cc_start: 0.7896 (mmt) cc_final: 0.7610 (mmp) REVERT: B 463 ASN cc_start: 0.7919 (t0) cc_final: 0.6898 (p0) REVERT: B 486 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 498 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6303 (mt-10) REVERT: C 296 MET cc_start: 0.8283 (mtp) cc_final: 0.7972 (mtt) REVERT: C 299 ARG cc_start: 0.7668 (mtp85) cc_final: 0.6616 (mmt90) REVERT: C 371 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6521 (mtm110) outliers start: 36 outliers final: 19 residues processed: 122 average time/residue: 0.6355 time to fit residues: 81.6337 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 74 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.116404 restraints weight = 8713.421| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.78 r_work: 0.3042 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8408 Z= 0.126 Angle : 0.556 11.581 11438 Z= 0.275 Chirality : 0.041 0.166 1285 Planarity : 0.005 0.039 1485 Dihedral : 5.801 52.617 1193 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.14 % Allowed : 16.67 % Favored : 79.20 % 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 (0.26), residues: 1065 helix: 1.35 (0.27), residues: 399 sheet: -0.77 (0.35), residues: 235 loop : -1.69 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.016 0.001 TYR B 421 PHE 0.014 0.001 PHE B 396 TRP 0.012 0.001 TRP C 360 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8408) covalent geometry : angle 0.55554 (11438) hydrogen bonds : bond 0.03452 ( 380) hydrogen bonds : angle 4.17107 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 175 ASP cc_start: 0.8756 (t0) cc_final: 0.8523 (t0) REVERT: A 221 LYS cc_start: 0.8330 (mttm) cc_final: 0.8052 (mttp) REVERT: A 267 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7587 (mtp180) REVERT: A 312 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 50 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7406 (pt0) REVERT: B 134 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 137 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7432 (mtp-110) REVERT: B 155 THR cc_start: 0.8107 (m) cc_final: 0.7826 (p) REVERT: B 179 THR cc_start: 0.7630 (p) cc_final: 0.7381 (t) REVERT: B 192 ASN cc_start: 0.7537 (m-40) cc_final: 0.7311 (t0) REVERT: B 205 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7280 (tpt170) REVERT: B 463 ASN cc_start: 0.7897 (t0) cc_final: 0.6873 (p0) REVERT: B 486 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.7071 (p0) REVERT: B 494 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.4647 (mtt180) REVERT: B 498 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6242 (mt-10) REVERT: C 296 MET cc_start: 0.8269 (mtp) cc_final: 0.7939 (mtt) REVERT: C 299 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6561 (mmt90) REVERT: C 371 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6496 (mtm110) outliers start: 35 outliers final: 19 residues processed: 118 average time/residue: 0.6070 time to fit residues: 75.7069 Evaluate side-chains 109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.151310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.119015 restraints weight = 8835.009| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.75 r_work: 0.3076 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8408 Z= 0.099 Angle : 0.521 10.161 11438 Z= 0.258 Chirality : 0.040 0.150 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.321 51.134 1191 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.31 % Allowed : 17.85 % Favored : 78.84 % 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: -0.22 (0.26), residues: 1065 helix: 1.63 (0.27), residues: 395 sheet: -0.51 (0.36), residues: 233 loop : -1.63 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.013 0.001 TYR A 53 PHE 0.014 0.001 PHE B 396 TRP 0.011 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8408) covalent geometry : angle 0.52095 (11438) hydrogen bonds : bond 0.02936 ( 380) hydrogen bonds : angle 4.04630 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 312 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 50 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7441 (pt0) REVERT: B 137 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7510 (mtp-110) REVERT: B 155 THR cc_start: 0.8092 (m) cc_final: 0.7839 (p) REVERT: B 167 GLU cc_start: 0.8382 (pt0) cc_final: 0.7646 (pp20) REVERT: B 178 ARG cc_start: 0.7161 (mtm110) cc_final: 0.5826 (mtm110) REVERT: B 192 ASN cc_start: 0.7511 (m-40) cc_final: 0.7302 (t0) REVERT: B 205 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7162 (tpt170) REVERT: B 283 MET cc_start: 0.7829 (mmt) cc_final: 0.7627 (mmp) REVERT: B 460 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7737 (mtmt) REVERT: B 463 ASN cc_start: 0.7860 (t0) cc_final: 0.6818 (p0) REVERT: B 498 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6256 (mt-10) REVERT: C 59 ARG cc_start: 0.7904 (mpp80) cc_final: 0.7478 (mpp80) REVERT: C 296 MET cc_start: 0.8229 (mtp) cc_final: 0.7929 (mtt) REVERT: C 299 ARG cc_start: 0.7667 (mtp85) cc_final: 0.6728 (mtt-85) REVERT: C 371 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.6524 (mtm110) outliers start: 28 outliers final: 14 residues processed: 115 average time/residue: 0.6584 time to fit residues: 79.6022 Evaluate side-chains 103 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.148783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117650 restraints weight = 8900.154| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.62 r_work: 0.3030 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8408 Z= 0.165 Angle : 0.581 9.206 11438 Z= 0.290 Chirality : 0.043 0.251 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.499 53.998 1188 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.55 % Allowed : 18.44 % Favored : 78.01 % 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: -0.36 (0.26), residues: 1065 helix: 1.40 (0.27), residues: 398 sheet: -0.60 (0.35), residues: 234 loop : -1.60 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.019 0.002 TYR A 53 PHE 0.016 0.002 PHE A 68 TRP 0.010 0.001 TRP C 360 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8408) covalent geometry : angle 0.58104 (11438) hydrogen bonds : bond 0.03851 ( 380) hydrogen bonds : angle 4.18604 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.289 Fit side-chains REVERT: A 312 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: B 50 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7562 (pt0) REVERT: B 134 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8197 (mt-10) REVERT: B 137 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7602 (mtp-110) REVERT: B 155 THR cc_start: 0.8172 (m) cc_final: 0.7913 (p) REVERT: B 178 ARG cc_start: 0.7405 (mtm110) cc_final: 0.5952 (mtm110) REVERT: B 205 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7417 (tpt170) REVERT: B 463 ASN cc_start: 0.7970 (t0) cc_final: 0.6924 (p0) REVERT: B 494 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.4832 (mtt180) REVERT: B 498 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6405 (mt-10) REVERT: C 296 MET cc_start: 0.8309 (mtp) cc_final: 0.7964 (mtt) REVERT: C 299 ARG cc_start: 0.7803 (mtp85) cc_final: 0.6890 (mtt-85) REVERT: C 371 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.6664 (mtm110) REVERT: C 418 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7266 (mt0) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 0.6338 time to fit residues: 74.8145 Evaluate side-chains 107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 0.0670 chunk 99 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN B 209 GLN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.118583 restraints weight = 8794.845| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.72 r_work: 0.3068 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8408 Z= 0.107 Angle : 0.535 8.970 11438 Z= 0.268 Chirality : 0.041 0.230 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.182 51.888 1188 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.96 % Allowed : 19.27 % Favored : 77.78 % 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: -0.12 (0.26), residues: 1065 helix: 1.62 (0.27), residues: 400 sheet: -0.34 (0.36), residues: 231 loop : -1.57 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.015 0.001 TYR A 53 PHE 0.014 0.001 PHE B 396 TRP 0.011 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8408) covalent geometry : angle 0.53488 (11438) hydrogen bonds : bond 0.03033 ( 380) hydrogen bonds : angle 4.03643 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7977 (ptt180) REVERT: A 312 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: B 50 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7464 (pt0) REVERT: B 137 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7420 (mtp-110) REVERT: B 155 THR cc_start: 0.8105 (m) cc_final: 0.7902 (p) REVERT: B 163 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: B 178 ARG cc_start: 0.7288 (mtm110) cc_final: 0.5913 (mtm110) REVERT: B 205 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7247 (tpt170) REVERT: B 460 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: B 463 ASN cc_start: 0.7871 (t0) cc_final: 0.6845 (p0) REVERT: B 498 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6239 (mt-10) REVERT: C 296 MET cc_start: 0.8252 (mtp) cc_final: 0.7890 (mtt) REVERT: C 299 ARG cc_start: 0.7707 (mtp85) cc_final: 0.6755 (mtt-85) REVERT: C 371 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6516 (mtm110) REVERT: C 418 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7261 (mt0) outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 0.6690 time to fit residues: 72.9687 Evaluate side-chains 102 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.149276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116799 restraints weight = 8760.632| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.74 r_work: 0.3057 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8408 Z= 0.134 Angle : 0.555 8.687 11438 Z= 0.277 Chirality : 0.042 0.226 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.270 53.174 1188 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.72 % Allowed : 19.50 % Favored : 77.78 % 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: -0.16 (0.26), residues: 1065 helix: 1.57 (0.27), residues: 400 sheet: -0.39 (0.36), residues: 233 loop : -1.56 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 308 TYR 0.017 0.001 TYR A 53 PHE 0.014 0.001 PHE A 68 TRP 0.010 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8408) covalent geometry : angle 0.55509 (11438) hydrogen bonds : bond 0.03463 ( 380) hydrogen bonds : angle 4.08895 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7804 (ptt180) REVERT: A 312 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 50 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7438 (pt0) REVERT: B 137 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7454 (mtp-110) REVERT: B 155 THR cc_start: 0.8109 (m) cc_final: 0.7900 (p) REVERT: B 163 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: B 167 GLU cc_start: 0.8469 (pt0) cc_final: 0.7783 (pp20) REVERT: B 178 ARG cc_start: 0.7294 (mtm110) cc_final: 0.5889 (mtm110) REVERT: B 205 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7247 (tpt170) REVERT: B 246 GLN cc_start: 0.8777 (tt0) cc_final: 0.8364 (tp-100) REVERT: B 283 MET cc_start: 0.7843 (mmt) cc_final: 0.7621 (mmp) REVERT: B 460 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7968 (mtmp) REVERT: B 463 ASN cc_start: 0.7895 (t0) cc_final: 0.6842 (p0) REVERT: B 498 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6270 (mt-10) REVERT: C 296 MET cc_start: 0.8242 (mtp) cc_final: 0.7877 (mtt) REVERT: C 299 ARG cc_start: 0.7701 (mtp85) cc_final: 0.6750 (mtt-85) REVERT: C 371 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.6501 (mtm110) REVERT: C 418 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7264 (mt0) outliers start: 23 outliers final: 16 residues processed: 106 average time/residue: 0.6638 time to fit residues: 73.7717 Evaluate side-chains 107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 36 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.151703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.120246 restraints weight = 8833.964| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.66 r_work: 0.3095 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8408 Z= 0.098 Angle : 0.521 8.709 11438 Z= 0.259 Chirality : 0.040 0.214 1285 Planarity : 0.004 0.038 1485 Dihedral : 4.971 51.410 1188 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.19 % Allowed : 19.39 % Favored : 77.42 % 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: 0.06 (0.26), residues: 1065 helix: 1.83 (0.27), residues: 395 sheet: -0.20 (0.37), residues: 231 loop : -1.53 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.014 0.001 TYR A 53 PHE 0.014 0.001 PHE B 396 TRP 0.011 0.001 TRP A 325 HIS 0.007 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8408) covalent geometry : angle 0.52075 (11438) hydrogen bonds : bond 0.02876 ( 380) hydrogen bonds : angle 3.98105 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.92 seconds wall clock time: 51 minutes 14.75 seconds (3074.75 seconds total)