Starting phenix.real_space_refine on Wed Mar 12 18:41:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wut_21918/03_2025/6wut_21918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wut_21918/03_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_21918/03_2025/6wut_21918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2025/6wut_21918.map" model { file = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_2025/6wut_21918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wut_21918/03_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-5624/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: 5.32, per 1000 atoms: 0.65 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: 1.74 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: 0.95 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: 2.50 Time building geometry restraints manager: 2.12 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: 0.700 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.060 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 : 0.854 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: 1.1664 time to fit residues: 213.4480 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 : 0.826 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119427 restraints weight = 8702.625| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.49 r_work: 0.3068 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.895 Fit side-chains REVERT: B 50 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7394 (pt0) REVERT: B 108 PHE cc_start: 0.6971 (m-80) cc_final: 0.6769 (m-80) REVERT: B 131 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7006 (mtt90) REVERT: B 134 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 137 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7659 (mtp-110) REVERT: B 155 THR cc_start: 0.8166 (m) cc_final: 0.7867 (p) REVERT: B 167 GLU cc_start: 0.8418 (pt0) cc_final: 0.8131 (pt0) REVERT: B 179 THR cc_start: 0.7763 (p) cc_final: 0.7440 (t) REVERT: B 205 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7515 (tpt170) REVERT: B 248 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8625 (p) REVERT: B 283 MET cc_start: 0.7973 (mmt) cc_final: 0.7735 (mmp) REVERT: B 463 ASN cc_start: 0.8064 (t0) cc_final: 0.7236 (p0) REVERT: B 498 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6383 (mt-10) REVERT: C 299 ARG cc_start: 0.7859 (mtp85) cc_final: 0.6831 (mmt90) REVERT: C 371 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.6733 (mtm110) REVERT: C 418 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7450 (mt0) outliers start: 40 outliers final: 18 residues processed: 137 average time/residue: 1.1946 time to fit residues: 174.1930 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 : 0.764 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 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: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.147827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.116522 restraints weight = 8941.841| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.63 r_work: 0.3069 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8408 Z= 0.214 Angle : 0.580 9.112 11438 Z= 0.291 Chirality : 0.042 0.177 1285 Planarity : 0.006 0.045 1485 Dihedral : 6.515 58.318 1202 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.55 % Allowed : 15.48 % Favored : 80.97 % 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: -1.40 (0.25), residues: 1065 helix: 0.57 (0.26), residues: 397 sheet: -1.28 (0.35), residues: 228 loop : -2.14 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.018 0.002 PHE A 27 TYR 0.014 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 127 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.790 Fit side-chains REVERT: A 206 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.8386 (mtp180) REVERT: A 229 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7939 (p0) REVERT: B 50 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7403 (pt0) REVERT: B 134 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 155 THR cc_start: 0.7981 (m) cc_final: 0.7751 (p) REVERT: B 167 GLU cc_start: 0.8450 (pt0) cc_final: 0.8172 (pt0) REVERT: B 179 THR cc_start: 0.7753 (p) cc_final: 0.7472 (t) REVERT: B 205 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7437 (tpt170) REVERT: B 283 MET cc_start: 0.7945 (mmt) cc_final: 0.7698 (mmp) REVERT: B 460 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: B 463 ASN cc_start: 0.7986 (t0) cc_final: 0.7052 (p0) REVERT: B 498 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6391 (mt-10) REVERT: C 59 ARG cc_start: 0.8174 (mpp80) cc_final: 0.7824 (mpp80) REVERT: C 299 ARG cc_start: 0.7791 (mtp85) cc_final: 0.6774 (mmt90) REVERT: C 371 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.6702 (mtm110) outliers start: 30 outliers final: 16 residues processed: 119 average time/residue: 1.3729 time to fit residues: 172.9101 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 363 ASN B 402 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.119250 restraints weight = 8806.898| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.55 r_work: 0.3049 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8408 Z= 0.231 Angle : 0.579 9.870 11438 Z= 0.289 Chirality : 0.042 0.178 1285 Planarity : 0.005 0.041 1485 Dihedral : 6.245 56.271 1196 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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 (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: -0.98 (0.26), residues: 1065 helix: 0.98 (0.27), residues: 398 sheet: -1.03 (0.35), residues: 226 loop : -1.96 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.004 0.001 HIS C 172 PHE 0.017 0.002 PHE A 27 TYR 0.016 0.002 TYR A 53 ARG 0.003 0.000 ARG A 241 *********************** 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 136 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.810 Fit side-chains REVERT: A 229 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7922 (p0) REVERT: A 312 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 50 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7433 (pt0) REVERT: B 134 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 155 THR cc_start: 0.8152 (m) cc_final: 0.7905 (p) REVERT: B 167 GLU cc_start: 0.8456 (pt0) cc_final: 0.8140 (pt0) REVERT: B 179 THR cc_start: 0.7783 (p) cc_final: 0.7514 (t) REVERT: B 205 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7444 (tpt170) REVERT: B 283 MET cc_start: 0.7927 (mmt) cc_final: 0.7679 (mmp) REVERT: B 463 ASN cc_start: 0.7967 (t0) cc_final: 0.7026 (p0) REVERT: B 498 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6386 (mt-10) REVERT: C 299 ARG cc_start: 0.7749 (mtp85) cc_final: 0.6716 (mmt90) REVERT: C 371 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.6650 (mtm110) outliers start: 36 outliers final: 21 residues processed: 128 average time/residue: 1.5016 time to fit residues: 203.6783 Evaluate side-chains 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 229 ASP 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 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 507 VAL Chi-restraints excluded: chain C residue -34 MET 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 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 73 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.149387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.117002 restraints weight = 8709.251| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.73 r_work: 0.3114 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8408 Z= 0.177 Angle : 0.551 10.936 11438 Z= 0.272 Chirality : 0.041 0.163 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.965 53.609 1196 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.78 % Allowed : 16.31 % 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 (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: -0.63 (0.26), residues: 1065 helix: 1.28 (0.27), residues: 399 sheet: -0.92 (0.35), residues: 235 loop : -1.75 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.006 0.001 HIS C 172 PHE 0.016 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 130 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7888 (p0) REVERT: A 312 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 50 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7202 (pt0) REVERT: B 134 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 155 THR cc_start: 0.8043 (m) cc_final: 0.7752 (p) REVERT: B 169 LEU cc_start: 0.8502 (mt) cc_final: 0.8188 (mp) REVERT: B 179 THR cc_start: 0.7580 (p) cc_final: 0.7375 (t) REVERT: B 192 ASN cc_start: 0.7513 (m-40) cc_final: 0.7292 (t0) REVERT: B 205 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7221 (tpt170) REVERT: B 463 ASN cc_start: 0.7871 (t0) cc_final: 0.6855 (p0) REVERT: B 498 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6288 (mt-10) REVERT: C 299 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6536 (mmt90) REVERT: C 371 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6383 (mtm110) outliers start: 32 outliers final: 19 residues processed: 122 average time/residue: 1.4666 time to fit residues: 190.2795 Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 -32 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN B 209 GLN B 363 ASN B 486 ASN B 504 GLN C 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.147249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.118083 restraints weight = 8750.416| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.59 r_work: 0.2999 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8408 Z= 0.340 Angle : 0.635 11.303 11438 Z= 0.317 Chirality : 0.045 0.199 1285 Planarity : 0.006 0.041 1485 Dihedral : 6.223 55.769 1193 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.61 % Allowed : 16.43 % Favored : 78.96 % 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 (0.26), residues: 1065 helix: 1.00 (0.27), residues: 398 sheet: -0.89 (0.35), residues: 230 loop : -1.83 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 360 HIS 0.006 0.001 HIS C 172 PHE 0.019 0.002 PHE A 68 TYR 0.021 0.002 TYR A 53 ARG 0.004 0.000 ARG B 292 *********************** 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 140 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.811 Fit side-chains REVERT: A 312 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 50 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7563 (pt0) REVERT: B 134 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 137 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7790 (mtp-110) REVERT: B 155 THR cc_start: 0.8252 (m) cc_final: 0.8035 (p) REVERT: B 179 THR cc_start: 0.7947 (p) cc_final: 0.7683 (t) REVERT: B 205 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7614 (tpt170) REVERT: B 283 MET cc_start: 0.7977 (mmt) cc_final: 0.7759 (mmp) REVERT: B 463 ASN cc_start: 0.7994 (t0) cc_final: 0.7095 (p0) REVERT: B 494 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.5059 (mtt180) REVERT: B 498 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6475 (mt-10) REVERT: C -24 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7424 (mt-10) REVERT: C 244 GLU cc_start: 0.7412 (tp30) cc_final: 0.6991 (mm-30) REVERT: C 299 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7126 (mtt-85) REVERT: C 371 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6907 (mtt90) REVERT: C 415 GLU cc_start: 0.6999 (mp0) cc_final: 0.6449 (tt0) outliers start: 39 outliers final: 25 residues processed: 132 average time/residue: 1.5448 time to fit residues: 215.7496 Evaluate side-chains 127 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 494 ARG 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 45 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.148470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.115346 restraints weight = 8762.003| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.81 r_work: 0.3050 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2307 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= 0.203 Angle : 0.567 11.909 11438 Z= 0.280 Chirality : 0.042 0.170 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.852 53.356 1193 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.66 % Allowed : 18.20 % Favored : 78.13 % 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: 1.30 (0.27), residues: 399 sheet: -0.75 (0.35), residues: 235 loop : -1.67 (0.27), residues: 431 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 0.016 0.001 TYR A 53 ARG 0.004 0.000 ARG B 292 *********************** 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 125 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.945 Fit side-chains REVERT: A 312 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 50 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7203 (pt0) REVERT: B 134 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 137 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7413 (mtp-110) REVERT: B 155 THR cc_start: 0.8098 (m) cc_final: 0.7767 (p) REVERT: B 167 GLU cc_start: 0.8458 (pt0) cc_final: 0.7730 (pp20) REVERT: B 179 THR cc_start: 0.7563 (p) cc_final: 0.7362 (t) REVERT: B 192 ASN cc_start: 0.7526 (m-40) cc_final: 0.7268 (t0) REVERT: B 205 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7202 (tpt170) REVERT: B 460 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8008 (mtmp) REVERT: B 463 ASN cc_start: 0.7866 (t0) cc_final: 0.6811 (p0) REVERT: B 486 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7081 (p0) REVERT: B 498 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6216 (mt-10) REVERT: C 296 MET cc_start: 0.8154 (mtp) cc_final: 0.7835 (mtt) REVERT: C 299 ARG cc_start: 0.7622 (mtp85) cc_final: 0.6677 (mtt-85) REVERT: C 371 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.6375 (mtm110) outliers start: 31 outliers final: 22 residues processed: 116 average time/residue: 1.2257 time to fit residues: 150.9937 Evaluate side-chains 116 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 236 GLU 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 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 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 -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 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: 0.0770 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 209 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 = 0.3554 r_free = 0.3554 target = 0.148512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115379 restraints weight = 8838.208| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.81 r_work: 0.3052 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2374 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= 0.203 Angle : 0.561 11.152 11438 Z= 0.277 Chirality : 0.041 0.169 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.590 53.546 1191 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.26 % Allowed : 17.61 % Favored : 78.13 % 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: -0.39 (0.26), residues: 1065 helix: 1.38 (0.27), residues: 399 sheet: -0.64 (0.35), residues: 235 loop : -1.60 (0.28), residues: 431 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 0.004 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 124 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 312 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7202 (mt-10) REVERT: B 50 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7254 (pt0) REVERT: B 134 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 137 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7418 (mtp-110) REVERT: B 178 ARG cc_start: 0.7317 (mtm110) cc_final: 0.5783 (mtm110) REVERT: B 192 ASN cc_start: 0.7514 (m-40) cc_final: 0.7253 (t0) REVERT: B 205 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7212 (tpt170) REVERT: B 463 ASN cc_start: 0.7859 (t0) cc_final: 0.6792 (p0) REVERT: B 498 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6226 (mt-10) REVERT: C 296 MET cc_start: 0.8165 (mtp) cc_final: 0.7838 (mtt) REVERT: C 299 ARG cc_start: 0.7621 (mtp85) cc_final: 0.6671 (mtt-85) REVERT: C 371 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6377 (mtm110) outliers start: 36 outliers final: 26 residues processed: 113 average time/residue: 1.3387 time to fit residues: 159.8789 Evaluate side-chains 114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 236 GLU 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 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 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 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 68 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.0170 chunk 85 optimal weight: 0.5980 overall best weight: 0.2134 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.153538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.121285 restraints weight = 8899.958| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.77 r_work: 0.3150 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8408 Z= 0.119 Angle : 0.512 11.022 11438 Z= 0.252 Chirality : 0.040 0.215 1285 Planarity : 0.005 0.040 1485 Dihedral : 4.964 50.478 1189 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.84 % Allowed : 19.15 % 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 (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: 0.00 (0.27), residues: 1065 helix: 1.79 (0.27), residues: 396 sheet: -0.34 (0.36), residues: 233 loop : -1.50 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 325 HIS 0.007 0.001 HIS C 172 PHE 0.016 0.001 PHE B 396 TYR 0.015 0.001 TYR B 421 ARG 0.003 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 122 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.213 Fit side-chains REVERT: A 43 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8173 (mm-40) REVERT: A 87 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7970 (ptt180) REVERT: B 50 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7330 (pt0) REVERT: B 137 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7448 (mtp-110) REVERT: B 167 GLU cc_start: 0.8485 (pt0) cc_final: 0.7771 (pp20) REVERT: B 178 ARG cc_start: 0.7160 (mtm110) cc_final: 0.5904 (mtm110) REVERT: B 192 ASN cc_start: 0.7439 (m-40) cc_final: 0.7228 (t0) REVERT: B 202 GLU cc_start: 0.8260 (tt0) cc_final: 0.7221 (mt-10) REVERT: B 205 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7001 (tpt170) REVERT: B 460 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7679 (mtmt) REVERT: B 463 ASN cc_start: 0.7818 (t0) cc_final: 0.6753 (p0) REVERT: B 494 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.4978 (mtt90) REVERT: B 498 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6292 (mt-10) REVERT: C 296 MET cc_start: 0.8086 (mtp) cc_final: 0.7856 (mtt) REVERT: C 299 ARG cc_start: 0.7639 (mtp85) cc_final: 0.6512 (mmt90) REVERT: C 371 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6438 (mtm110) outliers start: 24 outliers final: 8 residues processed: 115 average time/residue: 1.4020 time to fit residues: 171.3127 Evaluate side-chains 103 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 460 LYS 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 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: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 402 ASN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.148037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116454 restraints weight = 8782.817| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.64 r_work: 0.3094 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8408 Z= 0.263 Angle : 0.599 10.329 11438 Z= 0.296 Chirality : 0.043 0.223 1285 Planarity : 0.005 0.067 1485 Dihedral : 5.358 54.478 1188 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.13 % Allowed : 20.45 % 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: -0.19 (0.26), residues: 1065 helix: 1.52 (0.27), residues: 399 sheet: -0.50 (0.36), residues: 233 loop : -1.49 (0.28), residues: 433 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 B 240 ARG 0.017 0.000 ARG C 59 ********************** 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 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.782 Fit side-chains REVERT: A 87 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7804 (ptt180) REVERT: B 50 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7381 (pt0) REVERT: B 134 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 137 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7572 (mtp-110) REVERT: B 178 ARG cc_start: 0.7441 (mtm110) cc_final: 0.6018 (mtm110) REVERT: B 202 GLU cc_start: 0.8290 (tt0) cc_final: 0.7333 (mp0) REVERT: B 205 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7364 (tpt170) REVERT: B 463 ASN cc_start: 0.7953 (t0) cc_final: 0.6900 (p0) REVERT: B 494 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.4784 (mtt180) REVERT: B 498 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6352 (mt-10) REVERT: C 299 ARG cc_start: 0.7776 (mtp85) cc_final: 0.6872 (mtt-85) REVERT: C 371 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.6595 (mtm110) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 1.5102 time to fit residues: 174.9081 Evaluate side-chains 105 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 206 ARG 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 201 VAL Chi-restraints excluded: chain B residue 243 VAL 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 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 92 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 41 optimal weight: 8.9990 chunk 19 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 64 GLN B 209 GLN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.119406 restraints weight = 8888.479| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.74 r_work: 0.3111 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8408 Z= 0.146 Angle : 0.553 10.505 11438 Z= 0.271 Chirality : 0.041 0.216 1285 Planarity : 0.005 0.042 1485 Dihedral : 5.035 52.031 1188 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.01 % Allowed : 21.39 % Favored : 76.60 % 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: 0.03 (0.26), residues: 1065 helix: 1.79 (0.27), residues: 395 sheet: -0.30 (0.36), residues: 231 loop : -1.47 (0.27), residues: 439 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 B 396 TYR 0.014 0.001 TYR A 53 ARG 0.015 0.000 ARG C 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6448.73 seconds wall clock time: 113 minutes 39.55 seconds (6819.55 seconds total)