Starting phenix.real_space_refine on Wed Feb 14 00:51:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_21918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_21918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_21918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_21918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/02_2024/6wut_21918.pdb" } 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 Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 494": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.09, 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 - 3.50 Amino acid : False - 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: 2.92 Conformation dependent library (CDL) restraints added in 1.5 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: 0.87 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: 2.42 Time building geometry restraints manager: 3.19 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: 97.81 - 105.06: 208 105.06 - 112.32: 4221 112.32 - 119.58: 2763 119.58 - 126.83: 4098 126.83 - 134.09: 148 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 2.440 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 45 " model vdw 2.279 2.440 nonbonded pdb=" O HIS C 51 " pdb=" OG1 THR C 54 " model vdw 2.282 2.440 nonbonded pdb=" O PHE A 55 " pdb=" OG SER A 67 " model vdw 2.300 2.440 nonbonded pdb=" OE2 GLU C 20 " pdb=" OH TYR C 278 " model vdw 2.307 2.440 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 2.770 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.250 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 0.890 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: 1.1969 time to fit residues: 218.7615 Evaluate side-chains 129 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1499 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= 0.248 Angle : 0.615 8.408 11438 Z= 0.309 Chirality : 0.042 0.189 1285 Planarity : 0.007 0.056 1485 Dihedral : 8.317 58.682 1229 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.20 % Allowed : 14.89 % 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: -2.18 (0.24), residues: 1065 helix: -0.25 (0.25), residues: 396 sheet: -1.73 (0.34), residues: 227 loop : -2.35 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.021 0.002 PHE A 27 TYR 0.017 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 148 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 104 time to evaluate : 0.963 Fit side-chains REVERT: A 206 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7616 (ttp-110) REVERT: B 62 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (pt) REVERT: B 134 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 155 THR cc_start: 0.7964 (m) cc_final: 0.7686 (p) REVERT: B 167 GLU cc_start: 0.7734 (pt0) cc_final: 0.7415 (pt0) REVERT: B 179 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7491 (t) REVERT: B 205 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.7231 (tpt170) REVERT: B 248 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 283 MET cc_start: 0.7879 (mmt) cc_final: 0.7676 (mmp) REVERT: B 463 ASN cc_start: 0.7822 (t0) cc_final: 0.7313 (p0) REVERT: B 498 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5951 (mt-10) REVERT: C 299 ARG cc_start: 0.7454 (mtp85) cc_final: 0.6640 (mmt90) REVERT: C 371 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.6437 (mtm110) outliers start: 44 outliers final: 19 residues processed: 133 average time/residue: 1.1265 time to fit residues: 160.0537 Evaluate side-chains 114 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 179 THR 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 462 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 209 GLN B 402 ASN B 486 ASN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1823 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= 0.203 Angle : 0.566 8.857 11438 Z= 0.283 Chirality : 0.041 0.175 1285 Planarity : 0.005 0.044 1485 Dihedral : 6.624 57.523 1206 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.26 % Allowed : 16.19 % Favored : 79.55 % 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: -1.33 (0.25), residues: 1065 helix: 0.68 (0.27), residues: 396 sheet: -1.35 (0.34), residues: 232 loop : -2.07 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.004 0.001 HIS C 73 PHE 0.018 0.001 PHE A 27 TYR 0.016 0.001 TYR A 53 ARG 0.008 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 134 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 0.981 Fit side-chains REVERT: A 206 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7636 (mtp180) REVERT: A 229 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7320 (p0) REVERT: A 312 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: B 134 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 155 THR cc_start: 0.8045 (m) cc_final: 0.7796 (p) REVERT: B 167 GLU cc_start: 0.7757 (pt0) cc_final: 0.7404 (pt0) REVERT: B 179 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7565 (t) REVERT: B 205 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.7225 (tpt170) REVERT: B 246 GLN cc_start: 0.8641 (tt0) cc_final: 0.8393 (tt0) REVERT: B 283 MET cc_start: 0.7894 (mmt) cc_final: 0.7689 (mmp) REVERT: B 463 ASN cc_start: 0.7769 (t0) cc_final: 0.7199 (p0) REVERT: B 498 GLU cc_start: 0.6256 (mm-30) cc_final: 0.6025 (mt-10) REVERT: C 299 ARG cc_start: 0.7463 (mtp85) cc_final: 0.6639 (mmt90) REVERT: C 371 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6403 (mtm110) outliers start: 36 outliers final: 20 residues processed: 122 average time/residue: 1.2124 time to fit residues: 157.2762 Evaluate side-chains 113 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 A residue 312 GLU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 358 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8408 Z= 0.246 Angle : 0.586 9.892 11438 Z= 0.292 Chirality : 0.042 0.184 1285 Planarity : 0.005 0.040 1485 Dihedral : 6.270 54.829 1196 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.08 % Allowed : 15.96 % 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: -1.03 (0.26), residues: 1065 helix: 0.94 (0.27), residues: 398 sheet: -1.14 (0.35), residues: 230 loop : -1.94 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.004 0.001 HIS C 73 PHE 0.018 0.002 PHE A 27 TYR 0.018 0.002 TYR A 53 ARG 0.003 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 136 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 93 time to evaluate : 0.924 Fit side-chains REVERT: A 206 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7605 (ttp-110) REVERT: A 229 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7410 (p0) REVERT: A 312 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: B 129 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7851 (p) REVERT: B 134 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 167 GLU cc_start: 0.7783 (pt0) cc_final: 0.7402 (pt0) REVERT: B 169 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8081 (mt) REVERT: B 179 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7592 (t) REVERT: B 205 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7236 (tpt170) REVERT: B 283 MET cc_start: 0.7918 (mmt) cc_final: 0.7690 (mmp) REVERT: B 463 ASN cc_start: 0.7753 (t0) cc_final: 0.7130 (p0) REVERT: B 486 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7057 (p0) REVERT: B 498 GLU cc_start: 0.6268 (mm-30) cc_final: 0.6042 (mt-10) REVERT: C 299 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6704 (mmt90) REVERT: C 371 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6418 (mtm110) outliers start: 43 outliers final: 24 residues processed: 126 average time/residue: 1.1380 time to fit residues: 152.9329 Evaluate side-chains 120 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 109 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 A residue 320 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 462 THR 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 -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 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 504 GLN C 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2093 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= 0.225 Angle : 0.573 10.673 11438 Z= 0.284 Chirality : 0.042 0.169 1285 Planarity : 0.005 0.039 1485 Dihedral : 6.108 51.651 1196 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.08 % Allowed : 16.90 % 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: -0.80 (0.26), residues: 1065 helix: 1.10 (0.27), residues: 399 sheet: -0.92 (0.35), residues: 230 loop : -1.86 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.015 0.001 PHE A 27 TYR 0.016 0.001 TYR A 53 ARG 0.003 0.000 ARG B 375 *********************** 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 131 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7596 (ttp-110) REVERT: A 312 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.6972 (mt-10) REVERT: B 129 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.7825 (p) REVERT: B 134 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 167 GLU cc_start: 0.7751 (pt0) cc_final: 0.7357 (pt0) REVERT: B 179 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7498 (t) REVERT: B 205 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7226 (tpt170) REVERT: B 283 MET cc_start: 0.7930 (mmt) cc_final: 0.7682 (mmp) REVERT: B 463 ASN cc_start: 0.7737 (t0) cc_final: 0.7078 (p0) REVERT: B 486 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7234 (p0) REVERT: C 296 MET cc_start: 0.8027 (mtp) cc_final: 0.7753 (mtt) REVERT: C 299 ARG cc_start: 0.7411 (mtp85) cc_final: 0.6643 (mmt90) REVERT: C 371 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6383 (mtm110) outliers start: 43 outliers final: 28 residues processed: 120 average time/residue: 1.1798 time to fit residues: 150.8724 Evaluate side-chains 117 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 109 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 129 SER Chi-restraints excluded: chain B residue 179 THR 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 223 ASN Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 462 THR 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 40 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 172 ASN B 209 GLN C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8408 Z= 0.341 Angle : 0.638 11.394 11438 Z= 0.318 Chirality : 0.045 0.195 1285 Planarity : 0.006 0.042 1485 Dihedral : 6.382 53.019 1196 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.20 % Allowed : 17.38 % 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: -0.95 (0.25), residues: 1065 helix: 0.92 (0.27), residues: 398 sheet: -1.02 (0.34), residues: 234 loop : -1.87 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 360 HIS 0.005 0.001 HIS C 73 PHE 0.018 0.002 PHE A 68 TYR 0.020 0.002 TYR A 53 ARG 0.004 0.000 ARG A 241 *********************** 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 139 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 95 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7649 (ttp-110) REVERT: A 312 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7024 (mt-10) REVERT: B 134 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 137 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7408 (mtp-110) REVERT: B 167 GLU cc_start: 0.7732 (pt0) cc_final: 0.7381 (pt0) REVERT: B 179 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7508 (t) REVERT: B 205 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7210 (tpt170) REVERT: B 283 MET cc_start: 0.7923 (mmt) cc_final: 0.7669 (mmp) REVERT: B 463 ASN cc_start: 0.7732 (t0) cc_final: 0.7087 (p0) REVERT: B 498 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5896 (mt-10) REVERT: C 296 MET cc_start: 0.8032 (mtp) cc_final: 0.7715 (mtt) REVERT: C 299 ARG cc_start: 0.7489 (mtp85) cc_final: 0.6911 (mtt-85) REVERT: C 371 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.6459 (mtm110) REVERT: C 415 GLU cc_start: 0.6750 (mp0) cc_final: 0.6398 (tt0) outliers start: 44 outliers final: 29 residues processed: 129 average time/residue: 1.2003 time to fit residues: 164.7977 Evaluate side-chains 124 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 129 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 THR 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 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 462 THR 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 498 GLU 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 61 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2219 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= 0.237 Angle : 0.589 11.891 11438 Z= 0.290 Chirality : 0.042 0.171 1285 Planarity : 0.005 0.040 1485 Dihedral : 5.914 51.141 1194 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.44 % Allowed : 17.61 % Favored : 76.95 % 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: -0.71 (0.26), residues: 1065 helix: 1.16 (0.27), residues: 398 sheet: -0.84 (0.35), residues: 231 loop : -1.81 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.015 0.001 PHE B 396 TYR 0.017 0.001 TYR A 53 ARG 0.003 0.000 ARG A 241 *********************** 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 132 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 86 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 206 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7616 (ttp-110) REVERT: A 229 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7390 (p0) REVERT: A 312 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: B 134 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 137 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7281 (mtp-110) REVERT: B 167 GLU cc_start: 0.7709 (pt0) cc_final: 0.7356 (pt0) REVERT: B 179 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7497 (t) REVERT: B 205 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7255 (tpt170) REVERT: B 283 MET cc_start: 0.7920 (mmt) cc_final: 0.7676 (mmp) REVERT: B 463 ASN cc_start: 0.7724 (t0) cc_final: 0.7099 (p0) REVERT: B 498 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5977 (mt-10) REVERT: C 296 MET cc_start: 0.8007 (mtp) cc_final: 0.7681 (mtt) REVERT: C 299 ARG cc_start: 0.7468 (mtp85) cc_final: 0.6901 (mtt-85) REVERT: C 371 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.6419 (mtm110) outliers start: 46 outliers final: 30 residues processed: 121 average time/residue: 1.1972 time to fit residues: 154.6485 Evaluate side-chains 119 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 82 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 229 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 MET 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 179 THR 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 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 462 THR 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 498 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.0570 chunk 65 optimal weight: 0.0970 chunk 70 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 81 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 184 ASN B 209 GLN C 4 GLN C 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8408 Z= 0.124 Angle : 0.522 10.980 11438 Z= 0.254 Chirality : 0.039 0.137 1285 Planarity : 0.004 0.039 1485 Dihedral : 5.315 47.968 1194 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.31 % Allowed : 19.74 % Favored : 76.95 % 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: -0.27 (0.26), residues: 1065 helix: 1.67 (0.27), residues: 394 sheet: -0.61 (0.36), residues: 231 loop : -1.68 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 325 HIS 0.002 0.000 HIS C 51 PHE 0.015 0.001 PHE B 396 TYR 0.013 0.001 TYR A 53 ARG 0.004 0.000 ARG C 308 *********************** 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 129 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 0.997 Fit side-chains REVERT: A 87 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7410 (ptt180) REVERT: A 312 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6918 (mt-10) REVERT: B 129 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7711 (p) REVERT: B 134 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7998 (mt-10) REVERT: B 137 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7074 (mtp-110) REVERT: B 179 THR cc_start: 0.7713 (p) cc_final: 0.7433 (t) REVERT: B 202 GLU cc_start: 0.7221 (tt0) cc_final: 0.6982 (mt-10) REVERT: B 205 ARG cc_start: 0.7444 (ttm-80) cc_final: 0.7158 (tpt170) REVERT: B 246 GLN cc_start: 0.8313 (tt0) cc_final: 0.7903 (tp-100) REVERT: B 283 MET cc_start: 0.7924 (mmt) cc_final: 0.7704 (mmp) REVERT: B 463 ASN cc_start: 0.7682 (t0) cc_final: 0.7041 (p0) REVERT: C 59 ARG cc_start: 0.8038 (mpp80) cc_final: 0.7340 (mpp80) REVERT: C 296 MET cc_start: 0.7954 (mtp) cc_final: 0.7706 (mtt) REVERT: C 299 ARG cc_start: 0.7386 (mtp85) cc_final: 0.6785 (mtt-85) REVERT: C 371 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6404 (mtm110) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 1.2674 time to fit residues: 164.1401 Evaluate side-chains 103 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 462 THR 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 -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 0.0270 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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 B 402 ASN B 504 GLN C 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2469 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 : 0.563 10.486 11438 Z= 0.276 Chirality : 0.041 0.159 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.348 50.308 1190 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.96 % Allowed : 20.80 % Favored : 76.24 % 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: -0.24 (0.26), residues: 1065 helix: 1.56 (0.27), residues: 399 sheet: -0.51 (0.36), residues: 229 loop : -1.61 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.015 0.001 PHE B 396 TYR 0.018 0.001 TYR A 53 ARG 0.004 0.000 ARG C 308 *********************** 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 112 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.921 Fit side-chains REVERT: A 87 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7383 (ptt180) REVERT: A 229 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7395 (p0) REVERT: A 312 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: B 129 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 134 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 137 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7217 (mtp-110) REVERT: B 179 THR cc_start: 0.7756 (p) cc_final: 0.7488 (t) REVERT: B 205 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.7132 (tpt170) REVERT: B 246 GLN cc_start: 0.8520 (tt0) cc_final: 0.8140 (tp-100) REVERT: B 283 MET cc_start: 0.7934 (mmt) cc_final: 0.7701 (mmp) REVERT: B 463 ASN cc_start: 0.7720 (t0) cc_final: 0.7055 (p0) REVERT: C 296 MET cc_start: 0.7989 (mtp) cc_final: 0.7724 (mtt) REVERT: C 299 ARG cc_start: 0.7397 (mtp85) cc_final: 0.6797 (mtt-85) REVERT: C 371 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.6398 (mtm110) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 1.3341 time to fit residues: 148.4551 Evaluate side-chains 105 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 155 THR 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 364 ASP Chi-restraints excluded: chain B residue 462 THR 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 -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.0670 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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 504 GLN C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2569 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= 0.159 Angle : 0.540 10.295 11438 Z= 0.263 Chirality : 0.040 0.146 1285 Planarity : 0.005 0.038 1485 Dihedral : 5.154 49.066 1190 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.96 % Allowed : 21.28 % Favored : 75.77 % 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: -0.08 (0.26), residues: 1065 helix: 1.74 (0.27), residues: 395 sheet: -0.38 (0.36), residues: 229 loop : -1.56 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.002 0.001 HIS A 162 PHE 0.015 0.001 PHE B 396 TYR 0.016 0.001 TYR A 53 ARG 0.002 0.000 ARG C 308 ********************** 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 117 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.058 Fit side-chains REVERT: A 87 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7391 (ptt180) REVERT: A 312 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 129 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7762 (p) REVERT: B 131 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6606 (mtt-85) REVERT: B 134 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 179 THR cc_start: 0.7715 (p) cc_final: 0.7441 (t) REVERT: B 202 GLU cc_start: 0.7247 (tt0) cc_final: 0.6994 (mt-10) REVERT: B 205 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7142 (tpt170) REVERT: B 246 GLN cc_start: 0.8465 (tt0) cc_final: 0.8054 (tp-100) REVERT: B 283 MET cc_start: 0.7942 (mmt) cc_final: 0.7714 (mmp) REVERT: B 463 ASN cc_start: 0.7707 (t0) cc_final: 0.7038 (p0) REVERT: B 494 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.5007 (mtt180) REVERT: C 296 MET cc_start: 0.7978 (mtp) cc_final: 0.7701 (mtt) REVERT: C 299 ARG cc_start: 0.7419 (mtp85) cc_final: 0.6792 (mtt-85) REVERT: C 371 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6404 (mtm110) outliers start: 25 outliers final: 14 residues processed: 110 average time/residue: 1.3452 time to fit residues: 156.8024 Evaluate side-chains 107 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 SER Chi-restraints excluded: chain B residue 155 THR 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 364 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 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 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 64 GLN B 209 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 = 0.3571 r_free = 0.3571 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.117482 restraints weight = 8686.904| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.74 r_work: 0.3050 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2560 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= 0.190 Angle : 0.554 10.006 11438 Z= 0.273 Chirality : 0.041 0.154 1285 Planarity : 0.005 0.044 1485 Dihedral : 5.102 50.036 1188 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.60 % Allowed : 21.99 % Favored : 75.41 % 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: -0.10 (0.26), residues: 1065 helix: 1.64 (0.27), residues: 400 sheet: -0.35 (0.36), residues: 229 loop : -1.56 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.003 0.001 HIS C 73 PHE 0.014 0.001 PHE B 396 TYR 0.018 0.001 TYR A 53 ARG 0.006 0.000 ARG C 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.09 seconds wall clock time: 58 minutes 21.26 seconds (3501.26 seconds total)