Starting phenix.real_space_refine on Wed Feb 12 18:03:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_21918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_21918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_21918.map" model { file = "/net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_21918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wut_21918/02_2025/6wut_21918.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.11, per 1000 atoms: 0.62 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.44 Time building geometry restraints manager: 2.29 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- 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= 0.498 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 : 3.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.003 TRP C 360 HIS 0.009 0.002 HIS C 73 PHE 0.036 0.003 PHE B 396 TYR 0.016 0.003 TYR A 331 ARG 0.006 0.001 ARG A 205 *********************** 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 : 0.803 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: 1.2246 time to fit residues: 223.5264 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 : 0.932 ------------------------------------------------------------------------------- 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 90 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3565 r_free = 0.3565 target = 0.148860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119425 restraints weight = 8702.619| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.49 r_work: 0.3069 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8408 Z= 0.308 Angle : 0.656 8.503 11438 Z= 0.332 Chirality : 0.044 0.207 1285 Planarity : 0.007 0.055 1485 Dihedral : 8.397 58.768 1229 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.73 % Allowed : 13.59 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.24), residues: 1065 helix: -0.41 (0.25), residues: 402 sheet: -1.74 (0.34), residues: 227 loop : -2.36 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 360 HIS 0.004 0.001 HIS C 73 PHE 0.022 0.002 PHE A 27 TYR 0.019 0.002 TYR A 53 ARG 0.004 0.000 ARG B 375 *********************** 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 149 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.853 Fit side-chains REVERT: B 50 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7396 (pt0) REVERT: B 108 PHE cc_start: 0.6985 (m-80) cc_final: 0.6781 (m-80) REVERT: B 131 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.7009 (mtt90) REVERT: B 134 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 137 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7666 (mtp-110) REVERT: B 155 THR cc_start: 0.8167 (m) cc_final: 0.7870 (p) REVERT: B 167 GLU cc_start: 0.8415 (pt0) cc_final: 0.8129 (pt0) REVERT: B 179 THR cc_start: 0.7755 (p) cc_final: 0.7433 (t) REVERT: B 205 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7518 (tpt170) REVERT: B 248 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 283 MET cc_start: 0.7977 (mmt) cc_final: 0.7737 (mmp) REVERT: B 463 ASN cc_start: 0.8066 (t0) cc_final: 0.7233 (p0) REVERT: B 498 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6385 (mt-10) REVERT: C 299 ARG cc_start: 0.7865 (mtp85) cc_final: 0.6837 (mmt90) REVERT: C 371 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.6733 (mtm110) REVERT: C 418 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7452 (mt0) outliers start: 40 outliers final: 18 residues processed: 137 average time/residue: 1.2585 time to fit residues: 182.9851 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.149975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.120436 restraints weight = 8866.083| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.50 r_work: 0.3052 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1856 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= 0.243 Angle : 0.596 9.241 11438 Z= 0.300 Chirality : 0.043 0.186 1285 Planarity : 0.006 0.046 1485 Dihedral : 6.608 58.171 1202 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.66 % Allowed : 15.48 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.25), residues: 1065 helix: 0.44 (0.26), residues: 401 sheet: -1.29 (0.35), residues: 228 loop : -2.08 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 360 HIS 0.004 0.001 HIS C 73 PHE 0.019 0.002 PHE A 27 TYR 0.015 0.001 TYR A 53 ARG 0.004 0.000 ARG B 292 *********************** 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 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.877 Fit side-chains REVERT: A 206 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8408 (mtp180) REVERT: A 229 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 50 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7423 (pt0) REVERT: B 134 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 137 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7598 (mtp-110) REVERT: B 155 THR cc_start: 0.8004 (m) cc_final: 0.7793 (p) REVERT: B 167 GLU cc_start: 0.8472 (pt0) cc_final: 0.8204 (pt0) REVERT: B 179 THR cc_start: 0.7796 (p) cc_final: 0.7511 (t) REVERT: B 205 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7477 (tpt170) REVERT: B 283 MET cc_start: 0.7960 (mmt) cc_final: 0.7712 (mmp) REVERT: B 460 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8049 (mtmp) REVERT: B 463 ASN cc_start: 0.8000 (t0) cc_final: 0.7091 (p0) REVERT: B 498 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6389 (mt-10) REVERT: C 59 ARG cc_start: 0.8163 (mpp80) cc_final: 0.7800 (mpp80) REVERT: C 299 ARG cc_start: 0.7811 (mtp85) cc_final: 0.6808 (mmt90) REVERT: C 371 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.6758 (mtm110) REVERT: C 418 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7345 (mt0) outliers start: 31 outliers final: 17 residues processed: 120 average time/residue: 1.3786 time to fit residues: 175.2519 Evaluate side-chains 114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 137 ARG Chi-restraints excluded: chain B residue 181 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 460 LYS 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 287 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 overall best weight: 0.5520 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.118996 restraints weight = 8836.669| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.62 r_work: 0.3074 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8408 Z= 0.152 Angle : 0.534 9.905 11438 Z= 0.265 Chirality : 0.040 0.156 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.965 55.983 1197 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 16.90 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1065 helix: 1.10 (0.27), residues: 398 sheet: -1.04 (0.35), residues: 233 loop : -1.86 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.005 0.001 HIS C 172 PHE 0.016 0.001 PHE A 27 TYR 0.014 0.001 TYR B 421 ARG 0.004 0.000 ARG B 375 *********************** 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 128 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.843 Fit side-chains REVERT: A 206 ARG cc_start: 0.8708 (mtp-110) cc_final: 0.8363 (mtp180) REVERT: A 312 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 50 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7416 (pt0) REVERT: B 131 ARG cc_start: 0.7291 (mtt-85) cc_final: 0.6977 (mtt-85) REVERT: B 134 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 167 GLU cc_start: 0.8455 (pt0) cc_final: 0.8168 (pt0) REVERT: B 179 THR cc_start: 0.7693 (p) cc_final: 0.7458 (t) REVERT: B 205 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7378 (tpt170) REVERT: B 283 MET cc_start: 0.7912 (mmt) cc_final: 0.7668 (mmp) REVERT: B 463 ASN cc_start: 0.7942 (t0) cc_final: 0.6989 (p0) REVERT: B 498 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6379 (mt-10) REVERT: C 59 ARG cc_start: 0.8174 (mpp80) cc_final: 0.7871 (mpp80) REVERT: C 296 MET cc_start: 0.8261 (mtp) cc_final: 0.7988 (mtt) REVERT: C 299 ARG cc_start: 0.7715 (mtp85) cc_final: 0.6689 (mmt90) REVERT: C 371 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.6648 (mtm110) outliers start: 31 outliers final: 15 residues processed: 121 average time/residue: 1.2943 time to fit residues: 166.0153 Evaluate side-chains 107 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 181 SER 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 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER 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 73 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 402 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.150736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117732 restraints weight = 8691.717| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.77 r_work: 0.3067 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8408 Z= 0.167 Angle : 0.535 11.232 11438 Z= 0.265 Chirality : 0.040 0.157 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.682 52.911 1193 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.02 % Allowed : 17.38 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.26), residues: 1065 helix: 1.36 (0.27), residues: 399 sheet: -0.76 (0.35), residues: 231 loop : -1.73 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.005 0.001 HIS C 172 PHE 0.013 0.001 PHE A 27 TYR 0.014 0.001 TYR A 53 ARG 0.003 0.000 ARG B 292 *********************** 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 129 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.964 Fit side-chains REVERT: A 229 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7913 (p0) REVERT: A 312 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: B 50 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7246 (pt0) REVERT: B 134 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8114 (mt-10) REVERT: B 167 GLU cc_start: 0.8444 (pt0) cc_final: 0.8148 (pt0) REVERT: B 179 THR cc_start: 0.7609 (p) cc_final: 0.7391 (t) REVERT: B 192 ASN cc_start: 0.7528 (m-40) cc_final: 0.7305 (t0) REVERT: B 202 GLU cc_start: 0.8298 (tt0) cc_final: 0.7210 (mp0) REVERT: B 205 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7171 (tpt170) REVERT: B 283 MET cc_start: 0.7859 (mmt) cc_final: 0.7607 (mmp) REVERT: B 463 ASN cc_start: 0.7893 (t0) cc_final: 0.6880 (p0) REVERT: B 498 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6278 (mt-10) REVERT: C 296 MET cc_start: 0.8201 (mtp) cc_final: 0.7860 (mtt) REVERT: C 299 ARG cc_start: 0.7665 (mtp85) cc_final: 0.6525 (mmt90) REVERT: C 371 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6435 (mtm110) outliers start: 34 outliers final: 20 residues processed: 121 average time/residue: 1.3514 time to fit residues: 173.1321 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 229 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER 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 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 SER 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 58 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.145255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.113320 restraints weight = 8802.392| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.67 r_work: 0.3032 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8408 Z= 0.380 Angle : 0.646 9.294 11438 Z= 0.326 Chirality : 0.046 0.212 1285 Planarity : 0.006 0.040 1485 Dihedral : 6.247 56.216 1193 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.08 % Allowed : 16.55 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1065 helix: 0.98 (0.27), residues: 398 sheet: -0.83 (0.35), residues: 228 loop : -1.84 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 244 HIS 0.006 0.001 HIS C 172 PHE 0.020 0.002 PHE A 68 TYR 0.021 0.002 TYR A 53 ARG 0.004 0.000 ARG A 87 *********************** 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 150 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7719 (ptt180) REVERT: A 267 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: A 312 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: B 50 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7418 (pt0) REVERT: B 134 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8212 (mt-10) REVERT: B 137 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7802 (mtp-110) REVERT: B 167 GLU cc_start: 0.8500 (pt0) cc_final: 0.8219 (pt0) REVERT: B 169 LEU cc_start: 0.8524 (mt) cc_final: 0.8261 (mp) REVERT: B 179 THR cc_start: 0.7850 (p) cc_final: 0.7554 (t) REVERT: B 192 ASN cc_start: 0.7745 (m-40) cc_final: 0.7519 (t0) REVERT: B 205 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7408 (tpt170) REVERT: B 283 MET cc_start: 0.7925 (mmt) cc_final: 0.7661 (mmp) REVERT: B 463 ASN cc_start: 0.7953 (t0) cc_final: 0.6944 (p0) REVERT: B 486 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7394 (p0) REVERT: B 498 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6383 (mt-10) REVERT: C -24 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7358 (mt-10) REVERT: C 244 GLU cc_start: 0.7284 (tp30) cc_final: 0.6815 (mm-30) REVERT: C 296 MET cc_start: 0.8342 (mtp) cc_final: 0.8006 (mtt) REVERT: C 299 ARG cc_start: 0.7832 (mtp85) cc_final: 0.6975 (mtt-85) REVERT: C 371 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6655 (mtt90) REVERT: C 415 GLU cc_start: 0.7177 (mp0) cc_final: 0.6483 (tt0) REVERT: C 418 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7303 (mt0) outliers start: 43 outliers final: 25 residues processed: 140 average time/residue: 1.3657 time to fit residues: 202.2207 Evaluate side-chains 137 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 267 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER 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 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 194 ASN B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.148881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.115585 restraints weight = 8743.711| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.81 r_work: 0.3033 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2334 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= 0.191 Angle : 0.564 12.187 11438 Z= 0.277 Chirality : 0.041 0.167 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.615 53.055 1191 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.90 % Allowed : 18.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1065 helix: 1.32 (0.27), residues: 399 sheet: -0.64 (0.36), residues: 231 loop : -1.69 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.015 0.001 PHE A 27 TYR 0.015 0.001 TYR A 53 ARG 0.002 0.000 ARG C 308 *********************** 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 126 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7707 (ptt180) REVERT: A 312 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: B 50 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7202 (pt0) REVERT: B 134 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 169 LEU cc_start: 0.8486 (mt) cc_final: 0.8262 (mt) REVERT: B 178 ARG cc_start: 0.7164 (mtm110) cc_final: 0.5809 (mtm110) REVERT: B 192 ASN cc_start: 0.7701 (m-40) cc_final: 0.7397 (t0) REVERT: B 205 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7127 (tpt170) REVERT: B 463 ASN cc_start: 0.7863 (t0) cc_final: 0.6787 (p0) REVERT: B 486 ASN cc_start: 0.7458 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 498 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6261 (mt-10) REVERT: C 299 ARG cc_start: 0.7628 (mtp85) cc_final: 0.6663 (mtt-85) REVERT: C 371 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.6368 (mtm110) outliers start: 33 outliers final: 24 residues processed: 121 average time/residue: 1.4051 time to fit residues: 179.6310 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER 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 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.147114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.114623 restraints weight = 8850.205| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.72 r_work: 0.3013 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2320 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= 0.270 Angle : 0.599 11.387 11438 Z= 0.298 Chirality : 0.044 0.247 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.746 54.832 1191 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.49 % Allowed : 18.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1065 helix: 1.23 (0.27), residues: 398 sheet: -0.68 (0.35), residues: 233 loop : -1.67 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.016 0.002 PHE A 68 TYR 0.019 0.002 TYR A 53 ARG 0.005 0.000 ARG B 292 *********************** 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 134 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8290 (mtm110) cc_final: 0.7757 (ptt180) REVERT: A 312 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: B 50 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7363 (pt0) REVERT: B 134 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 167 GLU cc_start: 0.8472 (pt0) cc_final: 0.7759 (pp20) REVERT: B 178 ARG cc_start: 0.7455 (mtm110) cc_final: 0.5990 (mtm110) REVERT: B 192 ASN cc_start: 0.7744 (m-40) cc_final: 0.7510 (t0) REVERT: B 205 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7299 (tpt170) REVERT: B 463 ASN cc_start: 0.7934 (t0) cc_final: 0.6923 (p0) REVERT: B 486 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.7274 (p0) REVERT: B 498 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6303 (mt-10) REVERT: C 296 MET cc_start: 0.8254 (mtp) cc_final: 0.7981 (mtt) REVERT: C 299 ARG cc_start: 0.7750 (mtp85) cc_final: 0.6819 (mtt-85) REVERT: C 371 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.6552 (mtm110) REVERT: C 418 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7307 (mt0) outliers start: 38 outliers final: 26 residues processed: 125 average time/residue: 1.4007 time to fit residues: 184.6680 Evaluate side-chains 123 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER 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 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 157 THR 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 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 3 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.117681 restraints weight = 8878.496| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.78 r_work: 0.3061 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8408 Z= 0.153 Angle : 0.541 10.871 11438 Z= 0.266 Chirality : 0.041 0.226 1285 Planarity : 0.005 0.040 1485 Dihedral : 5.333 52.248 1191 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.55 % Allowed : 18.91 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1065 helix: 1.63 (0.27), residues: 394 sheet: -0.43 (0.36), residues: 231 loop : -1.61 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.015 0.001 PHE B 396 TYR 0.015 0.001 TYR A 53 ARG 0.005 0.000 ARG B 292 *********************** 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 120 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.929 Fit side-chains REVERT: A 87 ARG cc_start: 0.8312 (mtm110) cc_final: 0.7685 (ptt180) REVERT: A 312 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: B 50 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7282 (pt0) REVERT: B 134 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8048 (mt-10) REVERT: B 137 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (mtp-110) REVERT: B 178 ARG cc_start: 0.7364 (mtm110) cc_final: 0.5956 (mtm110) REVERT: B 205 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7202 (tpt170) REVERT: B 246 GLN cc_start: 0.8691 (tt0) cc_final: 0.8386 (tp-100) REVERT: B 463 ASN cc_start: 0.7850 (t0) cc_final: 0.6794 (p0) REVERT: B 486 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.7037 (OUTLIER) REVERT: B 494 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8628 (mpt180) REVERT: B 498 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6190 (mt-10) REVERT: C 59 ARG cc_start: 0.8051 (mpp80) cc_final: 0.7662 (mpp80) REVERT: C 296 MET cc_start: 0.8108 (mtp) cc_final: 0.7829 (mtt) REVERT: C 299 ARG cc_start: 0.7622 (mtp85) cc_final: 0.6485 (mmt90) REVERT: C 371 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6404 (mtm110) outliers start: 30 outliers final: 20 residues processed: 113 average time/residue: 1.4485 time to fit residues: 172.7371 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 137 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL 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 61 SER Chi-restraints excluded: chain C residue 157 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.117349 restraints weight = 8726.158| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.74 r_work: 0.3051 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2522 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= 0.188 Angle : 0.558 10.691 11438 Z= 0.275 Chirality : 0.042 0.221 1285 Planarity : 0.005 0.040 1485 Dihedral : 5.292 53.023 1190 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1065 helix: 1.66 (0.27), residues: 394 sheet: -0.44 (0.36), residues: 233 loop : -1.54 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.014 0.001 PHE B 396 TYR 0.017 0.001 TYR A 53 ARG 0.005 0.000 ARG B 292 ********************** 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 121 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7704 (ptt180) REVERT: A 312 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: B 50 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7327 (pt0) REVERT: B 178 ARG cc_start: 0.7405 (mtm110) cc_final: 0.5957 (mtm110) REVERT: B 192 ASN cc_start: 0.7716 (m-40) cc_final: 0.7473 (t0) REVERT: B 205 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7243 (tpt170) REVERT: B 246 GLN cc_start: 0.8812 (tt0) cc_final: 0.8510 (tp-100) REVERT: B 463 ASN cc_start: 0.7893 (t0) cc_final: 0.6856 (p0) REVERT: B 486 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.7075 (OUTLIER) REVERT: B 494 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.4648 (mtt180) REVERT: B 498 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6247 (mt-10) REVERT: C 296 MET cc_start: 0.8186 (mtp) cc_final: 0.7898 (mtt) REVERT: C 299 ARG cc_start: 0.7677 (mtp85) cc_final: 0.6730 (mtt-85) REVERT: C 371 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.6506 (mtm110) REVERT: C 418 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7305 (mt0) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 1.4534 time to fit residues: 173.0560 Evaluate side-chains 114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL 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 61 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 287 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 15 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 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 56 ASN B 209 GLN B 402 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.149890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116727 restraints weight = 8876.888| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.83 r_work: 0.3046 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2562 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= 0.188 Angle : 0.554 10.476 11438 Z= 0.273 Chirality : 0.042 0.216 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.208 53.028 1190 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.43 % Allowed : 19.74 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1065 helix: 1.68 (0.27), residues: 395 sheet: -0.38 (0.36), residues: 233 loop : -1.46 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.014 0.001 PHE B 396 TYR 0.017 0.001 TYR B 421 ARG 0.005 0.000 ARG B 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6296.40 seconds wall clock time: 111 minutes 24.83 seconds (6684.83 seconds total)