Starting phenix.real_space_refine on Mon Mar 11 05:50:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/03_2024/6qnu_4609.pdb" } resolution = 3.8 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= -0.000 sd= 0.008 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 22 5.16 5 C 4655 2.51 5 N 1169 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7250 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain breaks: 5 Time building chain proxies: 4.30, per 1000 atoms: 0.59 Number of scatterers: 7250 At special positions: 0 Unit cell: (94.963, 105.633, 93.896, 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 22 16.00 O 1404 8.00 N 1169 7.00 C 4655 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 2.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.583A pdb=" N ASN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.153A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.424A pdb=" N GLY E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL A 269 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.734A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N LEU C 305 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.652A pdb=" N PHE C 312 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197 removed outlier: 5.542A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.401A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG D 193 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR D 149 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.854A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 170 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.722A pdb=" N VAL D 222 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263 removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 324 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.511A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 190 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.724A pdb=" N ILE E 171 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.521A pdb=" N VAL E 222 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.681A pdb=" N GLY E 230 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277 188 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 2.68 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: 2260 1.34 - 1.46: 1349 1.46 - 1.57: 3752 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7399 Sorted by residual: bond pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CA THR A 304 " pdb=" CB THR A 304 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.95e+00 bond pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.64e+00 bond pdb=" CA TYR E 158 " pdb=" C TYR E 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.63e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 231 106.78 - 113.59: 4100 113.59 - 120.40: 2620 120.40 - 127.20: 3032 127.20 - 134.01: 67 Bond angle restraints: 10050 Sorted by residual: angle pdb=" C ALA A 303 " pdb=" N THR A 304 " pdb=" CA THR A 304 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN D 219 " pdb=" N ILE D 220 " pdb=" CA ILE D 220 " ideal model delta sigma weight residual 122.13 130.06 -7.93 1.85e+00 2.92e-01 1.84e+01 angle pdb=" N ILE D 315 " pdb=" CA ILE D 315 " pdb=" C ILE D 315 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N TRP D 257 " pdb=" CA TRP D 257 " pdb=" C TRP D 257 " ideal model delta sigma weight residual 114.04 109.06 4.98 1.24e+00 6.50e-01 1.62e+01 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3940 16.84 - 33.69: 390 33.69 - 50.53: 66 50.53 - 67.37: 11 67.37 - 84.22: 6 Dihedral angle restraints: 4413 sinusoidal: 1724 harmonic: 2689 Sorted by residual: dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CA ASP D 218 " pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta harmonic sigma weight residual -180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 845 0.053 - 0.106: 236 0.106 - 0.159: 77 0.159 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA TYR E 158 " pdb=" N TYR E 158 " pdb=" C TYR E 158 " pdb=" CB TYR E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE C 306 " pdb=" CA ILE C 306 " pdb=" CG1 ILE C 306 " pdb=" CG2 ILE C 306 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1167 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C LYS B 275 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 219 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASN E 219 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN E 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 220 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 308 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 309 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2300 2.84 - 3.35: 5486 3.35 - 3.87: 11611 3.87 - 4.38: 12135 4.38 - 4.90: 22568 Nonbonded interactions: 54100 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.324 2.440 nonbonded pdb=" OE1 GLU C 194 " pdb=" OH TYR C 196 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR C 135 " pdb=" O LEU C 158 " model vdw 2.349 2.440 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.351 2.440 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.392 2.440 ... (remaining 54095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } ncs_group { reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ ugh 233 or resid 238 through 291 or resid 299 through 331)) selection = chain 'E' } 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 group one per residue 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: 0.390 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: 0.020 Extract box with map and model: 2.160 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.030 Find NCS groups from input model: 0.650 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.004 0.045 7399 Z= 0.286 Angle : 0.909 10.852 10050 Z= 0.494 Chirality : 0.057 0.264 1170 Planarity : 0.006 0.054 1269 Dihedral : 13.913 84.215 2671 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.61 % Allowed : 5.89 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.05 (0.24), residues: 880 helix: -4.32 (0.26), residues: 24 sheet: -1.61 (0.27), residues: 323 loop : -3.50 (0.21), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.005 0.001 HIS B 246 PHE 0.019 0.002 PHE D 301 TYR 0.022 0.002 TYR A 170 ARG 0.004 0.001 ARG E 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8376 (mttt) cc_final: 0.8081 (mtpp) REVERT: A 163 ASN cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: B 150 GLN cc_start: 0.8680 (mp-120) cc_final: 0.8340 (mt0) REVERT: D 112 GLN cc_start: 0.7803 (mt0) cc_final: 0.7533 (tt0) REVERT: D 164 LEU cc_start: 0.8552 (tp) cc_final: 0.8283 (tp) REVERT: E 208 GLN cc_start: 0.7162 (mt0) cc_final: 0.6729 (mt0) outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.2624 time to fit residues: 60.7492 Evaluate side-chains 124 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 151 ASN A 168 ASN A 246 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 210 GLN D 236 GLN E 126 HIS E 183 HIS E 217 ASN E 312 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7399 Z= 0.310 Angle : 0.659 6.724 10050 Z= 0.342 Chirality : 0.046 0.182 1170 Planarity : 0.004 0.038 1269 Dihedral : 6.202 30.757 973 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.82 % Allowed : 13.99 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.49 (0.25), residues: 880 helix: -2.83 (0.74), residues: 18 sheet: -1.54 (0.27), residues: 334 loop : -2.96 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 134 HIS 0.011 0.001 HIS B 246 PHE 0.012 0.002 PHE C 197 TYR 0.017 0.002 TYR A 170 ARG 0.005 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 162 LYS cc_start: 0.8371 (mttt) cc_final: 0.8053 (mtpp) REVERT: B 150 GLN cc_start: 0.8697 (mp-120) cc_final: 0.8313 (mt0) REVERT: C 147 TYR cc_start: 0.6614 (t80) cc_final: 0.5998 (t80) REVERT: D 112 GLN cc_start: 0.7823 (mt0) cc_final: 0.7309 (tt0) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.2107 time to fit residues: 39.1479 Evaluate side-chains 125 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 249 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 246 HIS C 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7399 Z= 0.307 Angle : 0.646 8.961 10050 Z= 0.332 Chirality : 0.047 0.166 1170 Planarity : 0.004 0.033 1269 Dihedral : 6.044 29.449 973 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.54 % Allowed : 13.99 % Favored : 81.47 % 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: -3.16 (0.26), residues: 880 helix: -1.92 (0.96), residues: 18 sheet: -1.29 (0.28), residues: 333 loop : -2.78 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 134 HIS 0.006 0.001 HIS B 246 PHE 0.020 0.002 PHE C 197 TYR 0.017 0.002 TYR A 170 ARG 0.004 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 0.962 Fit side-chains REVERT: A 162 LYS cc_start: 0.8388 (mttt) cc_final: 0.8100 (mtpp) REVERT: B 150 GLN cc_start: 0.8731 (mp-120) cc_final: 0.8295 (mt0) REVERT: C 147 TYR cc_start: 0.6577 (t80) cc_final: 0.6033 (t80) REVERT: E 257 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.8350 (t-100) outliers start: 37 outliers final: 27 residues processed: 139 average time/residue: 0.2247 time to fit residues: 42.2417 Evaluate side-chains 133 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 48 optimal weight: 0.3980 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.218 Angle : 0.598 7.645 10050 Z= 0.306 Chirality : 0.046 0.163 1170 Planarity : 0.004 0.029 1269 Dihedral : 5.706 27.190 973 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.29 % Allowed : 16.81 % Favored : 78.90 % 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: -2.87 (0.27), residues: 880 helix: -1.03 (1.10), residues: 19 sheet: -1.26 (0.27), residues: 343 loop : -2.48 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 134 HIS 0.002 0.001 HIS E 273 PHE 0.019 0.001 PHE D 247 TYR 0.015 0.001 TYR A 170 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 0.886 Fit side-chains REVERT: A 162 LYS cc_start: 0.8298 (mttt) cc_final: 0.7997 (mtpp) REVERT: A 246 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6243 (m90) REVERT: B 150 GLN cc_start: 0.8636 (mp-120) cc_final: 0.8200 (mt0) REVERT: C 147 TYR cc_start: 0.6221 (t80) cc_final: 0.5796 (t80) REVERT: C 150 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7533 (mm-40) REVERT: C 314 TYR cc_start: 0.8553 (p90) cc_final: 0.8301 (p90) REVERT: E 257 TRP cc_start: 0.8727 (OUTLIER) cc_final: 0.8322 (t-100) outliers start: 35 outliers final: 23 residues processed: 138 average time/residue: 0.1786 time to fit residues: 33.7498 Evaluate side-chains 130 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.0670 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7399 Z= 0.300 Angle : 0.628 6.638 10050 Z= 0.322 Chirality : 0.047 0.158 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.778 28.719 973 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.64 % Allowed : 17.67 % Favored : 76.69 % 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: -2.82 (0.27), residues: 880 helix: -0.86 (1.13), residues: 19 sheet: -1.14 (0.28), residues: 331 loop : -2.51 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 290 HIS 0.006 0.001 HIS A 246 PHE 0.020 0.002 PHE D 247 TYR 0.023 0.002 TYR B 179 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 108 time to evaluate : 0.930 Fit side-chains REVERT: A 162 LYS cc_start: 0.8354 (mttt) cc_final: 0.8047 (mtpp) REVERT: B 150 GLN cc_start: 0.8657 (mp-120) cc_final: 0.8208 (mt0) REVERT: C 314 TYR cc_start: 0.8545 (p90) cc_final: 0.8292 (p90) REVERT: D 183 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.6532 (m-70) REVERT: E 257 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8450 (t-100) outliers start: 46 outliers final: 39 residues processed: 142 average time/residue: 0.1870 time to fit residues: 36.2618 Evaluate side-chains 147 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 106 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 130 ASN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 273 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7399 Z= 0.165 Angle : 0.549 6.370 10050 Z= 0.281 Chirality : 0.044 0.154 1170 Planarity : 0.004 0.028 1269 Dihedral : 5.218 24.607 973 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.05 % Allowed : 18.65 % Favored : 77.30 % 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: -2.66 (0.27), residues: 880 helix: -1.88 (0.85), residues: 26 sheet: -1.10 (0.27), residues: 337 loop : -2.30 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 134 HIS 0.004 0.001 HIS A 246 PHE 0.020 0.001 PHE D 247 TYR 0.027 0.001 TYR B 179 ARG 0.007 0.001 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 0.928 Fit side-chains REVERT: A 162 LYS cc_start: 0.8168 (mttt) cc_final: 0.7843 (mtpp) REVERT: A 163 ASN cc_start: 0.8718 (t0) cc_final: 0.8463 (t0) REVERT: B 150 GLN cc_start: 0.8633 (mp-120) cc_final: 0.8212 (mt0) REVERT: E 257 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.8325 (t-100) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.1817 time to fit residues: 34.5166 Evaluate side-chains 127 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.3980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7399 Z= 0.199 Angle : 0.575 6.340 10050 Z= 0.292 Chirality : 0.045 0.159 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.108 25.861 972 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.91 % Allowed : 18.65 % Favored : 76.44 % 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: -2.55 (0.27), residues: 880 helix: -1.72 (0.88), residues: 26 sheet: -1.05 (0.28), residues: 339 loop : -2.21 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 290 HIS 0.002 0.001 HIS E 126 PHE 0.018 0.001 PHE D 247 TYR 0.015 0.001 TYR B 179 ARG 0.007 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 0.920 Fit side-chains REVERT: A 162 LYS cc_start: 0.8180 (mttt) cc_final: 0.7870 (mtpp) REVERT: A 163 ASN cc_start: 0.8736 (t0) cc_final: 0.8461 (t0) REVERT: B 150 GLN cc_start: 0.8671 (mp-120) cc_final: 0.8229 (mt0) REVERT: B 272 MET cc_start: 0.8353 (tmm) cc_final: 0.7691 (tmm) REVERT: C 314 TYR cc_start: 0.8547 (p90) cc_final: 0.8263 (p90) REVERT: E 257 TRP cc_start: 0.8781 (OUTLIER) cc_final: 0.8443 (t-100) outliers start: 40 outliers final: 35 residues processed: 138 average time/residue: 0.1741 time to fit residues: 33.3074 Evaluate side-chains 139 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7399 Z= 0.197 Angle : 0.572 9.403 10050 Z= 0.289 Chirality : 0.045 0.152 1170 Planarity : 0.004 0.032 1269 Dihedral : 5.044 25.338 972 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 5.28 % Allowed : 18.16 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.48 (0.27), residues: 880 helix: -1.74 (0.88), residues: 26 sheet: -0.98 (0.28), residues: 337 loop : -2.18 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 290 HIS 0.004 0.001 HIS E 126 PHE 0.016 0.001 PHE D 247 TYR 0.014 0.001 TYR A 170 ARG 0.007 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 106 time to evaluate : 0.840 Fit side-chains REVERT: A 162 LYS cc_start: 0.8166 (mttt) cc_final: 0.7843 (mtpp) REVERT: A 163 ASN cc_start: 0.8735 (t0) cc_final: 0.8451 (t0) REVERT: B 150 GLN cc_start: 0.8620 (mp-120) cc_final: 0.8162 (mt0) REVERT: C 314 TYR cc_start: 0.8531 (p90) cc_final: 0.8243 (p90) REVERT: E 257 TRP cc_start: 0.8803 (OUTLIER) cc_final: 0.8477 (t-100) outliers start: 43 outliers final: 37 residues processed: 143 average time/residue: 0.1593 time to fit residues: 31.6498 Evaluate side-chains 140 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7399 Z= 0.215 Angle : 0.587 9.033 10050 Z= 0.297 Chirality : 0.045 0.153 1170 Planarity : 0.004 0.026 1269 Dihedral : 5.087 26.202 972 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.15 % Allowed : 19.02 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.28), residues: 880 helix: -1.72 (0.89), residues: 26 sheet: -0.97 (0.28), residues: 337 loop : -2.16 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 290 HIS 0.005 0.001 HIS E 126 PHE 0.015 0.001 PHE D 247 TYR 0.014 0.001 TYR A 170 ARG 0.005 0.001 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 0.969 Fit side-chains REVERT: A 162 LYS cc_start: 0.8206 (mttt) cc_final: 0.7896 (mtpp) REVERT: A 163 ASN cc_start: 0.8732 (t0) cc_final: 0.8463 (t0) REVERT: A 246 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.5866 (m90) REVERT: B 150 GLN cc_start: 0.8623 (mp-120) cc_final: 0.8178 (mt0) REVERT: C 314 TYR cc_start: 0.8538 (p90) cc_final: 0.8254 (p90) REVERT: E 257 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.8514 (t-100) outliers start: 42 outliers final: 38 residues processed: 141 average time/residue: 0.1819 time to fit residues: 35.0280 Evaluate side-chains 144 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.0030 chunk 10 optimal weight: 5.9990 overall best weight: 0.5112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7399 Z= 0.141 Angle : 0.550 9.486 10050 Z= 0.278 Chirality : 0.044 0.158 1170 Planarity : 0.003 0.039 1269 Dihedral : 4.752 23.158 972 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.56 % Allowed : 21.10 % Favored : 75.34 % 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: -2.30 (0.28), residues: 880 helix: -1.85 (0.82), residues: 26 sheet: -0.85 (0.28), residues: 349 loop : -2.05 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 134 HIS 0.004 0.001 HIS A 246 PHE 0.015 0.001 PHE D 247 TYR 0.012 0.001 TYR A 170 ARG 0.007 0.000 ARG B 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.945 Fit side-chains REVERT: A 162 LYS cc_start: 0.7990 (mttt) cc_final: 0.7737 (mtpp) REVERT: A 163 ASN cc_start: 0.8675 (t0) cc_final: 0.8397 (t0) REVERT: A 246 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5923 (m90) REVERT: B 150 GLN cc_start: 0.8642 (mp-120) cc_final: 0.8169 (mt0) REVERT: C 273 LEU cc_start: 0.8032 (mm) cc_final: 0.7802 (mt) REVERT: D 250 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6252 (m-30) REVERT: E 257 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.8370 (t-100) outliers start: 29 outliers final: 22 residues processed: 141 average time/residue: 0.1768 time to fit residues: 34.2098 Evaluate side-chains 133 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 257 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN E 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138958 restraints weight = 10724.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.141485 restraints weight = 6859.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.143277 restraints weight = 4598.957| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7399 Z= 0.160 Angle : 0.560 9.368 10050 Z= 0.282 Chirality : 0.044 0.150 1170 Planarity : 0.003 0.031 1269 Dihedral : 4.739 24.617 972 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.56 % Allowed : 21.47 % Favored : 74.97 % 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: -2.19 (0.28), residues: 880 helix: -1.81 (0.83), residues: 26 sheet: -0.76 (0.28), residues: 350 loop : -2.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 134 HIS 0.010 0.001 HIS A 246 PHE 0.015 0.001 PHE D 247 TYR 0.020 0.001 TYR B 179 ARG 0.007 0.001 ARG B 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.67 seconds wall clock time: 32 minutes 31.39 seconds (1951.39 seconds total)