Starting phenix.real_space_refine on Tue Mar 3 18:24:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.map" model { file = "/net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nf8_49355/03_2026/9nf8_49355.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 45 5.49 5 S 41 5.16 5 C 4732 2.51 5 N 1327 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7726 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4166 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain breaks: 3 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2589 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 6, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 971 Classifications: {'RNA': 46} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 17, 'rna3p_pyr': 18} Link IDs: {'rna2p': 11, 'rna3p': 34} Chain breaks: 3 Time building chain proxies: 1.66, per 1000 atoms: 0.21 Number of scatterers: 7726 At special positions: 0 Unit cell: (83.448, 105.408, 139.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 45 15.00 O 1581 8.00 N 1327 7.00 C 4732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 275.2 milliseconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 56.8% alpha, 7.5% beta 12 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.599A pdb=" N GLU A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.083A pdb=" N ALA A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 121 through 139 removed outlier: 3.664A pdb=" N LEU A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.571A pdb=" N ALA A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 222 through 236 removed outlier: 3.966A pdb=" N LYS A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.608A pdb=" N VAL A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.774A pdb=" N GLN A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.554A pdb=" N ASN A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.788A pdb=" N ILE A 324 " --> pdb=" O HIS A 320 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.064A pdb=" N TYR A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.513A pdb=" N THR A 404 " --> pdb=" O CYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 4.196A pdb=" N MET A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.636A pdb=" N ALA A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 487 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.817A pdb=" N VAL A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 25 removed outlier: 3.643A pdb=" N LEU B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.619A pdb=" N ILE B 127 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.565A pdb=" N PHE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 228 removed outlier: 3.550A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 253 removed outlier: 3.617A pdb=" N LEU B 249 " --> pdb=" O CYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 removed outlier: 3.653A pdb=" N ALA B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 336 removed outlier: 3.525A pdb=" N PHE B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 removed outlier: 4.358A pdb=" N ALA A 414 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A 413 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 373 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 415 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 375 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 496 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET A 519 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 498 " --> pdb=" O MET A 519 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.767A pdb=" N ASN B 139 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 115 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 263 removed outlier: 6.860A pdb=" N LEU B 274 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 262 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) 321 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2213 1.33 - 1.45: 1334 1.45 - 1.57: 4245 1.57 - 1.69: 87 1.69 - 1.81: 66 Bond restraints: 7945 Sorted by residual: bond pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" CA PHE A 473 " pdb=" CB PHE A 473 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.54e+00 bond pdb=" C ILE A 440 " pdb=" N PRO A 441 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.47e+00 bond pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CB GLN B 198 " pdb=" CG GLN B 198 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.14e-01 ... (remaining 7940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10719 1.74 - 3.48: 148 3.48 - 5.22: 14 5.22 - 6.96: 6 6.96 - 8.69: 2 Bond angle restraints: 10889 Sorted by residual: angle pdb=" N LEU B 79 " pdb=" CA LEU B 79 " pdb=" C LEU B 79 " ideal model delta sigma weight residual 114.09 107.97 6.12 1.55e+00 4.16e-01 1.56e+01 angle pdb=" CA GLU A 117 " pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " ideal model delta sigma weight residual 114.10 121.01 -6.91 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA GLU A 223 " pdb=" CB GLU A 223 " pdb=" CG GLU A 223 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 angle pdb=" CB GLU A 117 " pdb=" CG GLU A 117 " pdb=" CD GLU A 117 " ideal model delta sigma weight residual 112.60 117.44 -4.84 1.70e+00 3.46e-01 8.11e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 124.99 -8.69 3.50e+00 8.16e-02 6.17e+00 ... (remaining 10884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 4117 20.31 - 40.61: 589 40.61 - 60.91: 177 60.91 - 81.22: 57 81.22 - 101.52: 10 Dihedral angle restraints: 4950 sinusoidal: 2503 harmonic: 2447 Sorted by residual: dihedral pdb=" CA GLN A 75 " pdb=" C GLN A 75 " pdb=" N GLU A 76 " pdb=" CA GLU A 76 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER A 292 " pdb=" C SER A 292 " pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR A 169 " pdb=" C THR A 169 " pdb=" N LYS A 170 " pdb=" CA LYS A 170 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1028 0.045 - 0.091: 193 0.091 - 0.136: 37 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB VAL A 254 " pdb=" CA VAL A 254 " pdb=" CG1 VAL A 254 " pdb=" CG2 VAL A 254 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PRO A 441 " pdb=" N PRO A 441 " pdb=" C PRO A 441 " pdb=" CB PRO A 441 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA LEU A 449 " pdb=" N LEU A 449 " pdb=" C LEU A 449 " pdb=" CB LEU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1257 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 121 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 122 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 253 " 0.008 2.00e-02 2.50e+03 9.64e-03 1.62e+00 pdb=" CG PHE B 253 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 253 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 253 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 253 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 253 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 253 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 510 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 511 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.016 5.00e-02 4.00e+02 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 135 2.65 - 3.21: 6935 3.21 - 3.78: 11983 3.78 - 4.34: 16600 4.34 - 4.90: 26022 Nonbonded interactions: 61675 Sorted by model distance: nonbonded pdb=" OE1 GLN A 7 " pdb=" OG1 THR A 472 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THR A 507 " pdb=" OD1 ASP A 518 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASN A 391 " pdb=" OG1 THR A 394 " model vdw 2.209 3.040 nonbonded pdb=" O HIS B 250 " pdb=" OG SER B 254 " model vdw 2.257 3.040 nonbonded pdb=" N GLU B 281 " pdb=" OE1 GLU B 281 " model vdw 2.266 3.120 ... (remaining 61670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.003 0.039 7945 Z= 0.129 Angle : 0.504 8.694 10889 Z= 0.263 Chirality : 0.037 0.227 1260 Planarity : 0.003 0.036 1212 Dihedral : 20.663 101.524 3356 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.66 % Allowed : 32.16 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.29), residues: 829 helix: -0.31 (0.24), residues: 441 sheet: -0.84 (0.61), residues: 74 loop : -1.18 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 120 TYR 0.011 0.001 TYR A 23 PHE 0.022 0.001 PHE B 253 TRP 0.007 0.001 TRP A 144 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7945) covalent geometry : angle 0.50396 (10889) hydrogen bonds : bond 0.26566 ( 350) hydrogen bonds : angle 7.64929 ( 980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7846 (mmt) cc_final: 0.7524 (mmt) REVERT: A 55 LEU cc_start: 0.8638 (mm) cc_final: 0.8418 (mp) REVERT: A 69 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7839 (ptm160) REVERT: A 72 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 218 LEU cc_start: 0.7161 (mm) cc_final: 0.6848 (mm) REVERT: A 272 LEU cc_start: 0.8055 (pp) cc_final: 0.7803 (pp) REVERT: A 316 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8018 (ttpt) REVERT: A 399 MET cc_start: 0.8753 (tpt) cc_final: 0.8233 (tpt) REVERT: A 411 TYR cc_start: 0.8227 (t80) cc_final: 0.7883 (t80) REVERT: A 455 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 490 MET cc_start: 0.7672 (ptm) cc_final: 0.7342 (ppp) REVERT: B 9 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7619 (mmtm) REVERT: B 54 LYS cc_start: 0.6494 (mmtt) cc_final: 0.6288 (mmtt) REVERT: B 74 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7267 (ttpp) REVERT: B 81 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6793 (tp30) REVERT: B 191 LYS cc_start: 0.7315 (mmmm) cc_final: 0.6989 (mmtm) REVERT: B 214 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8597 (ttpp) REVERT: B 216 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8475 (tmmt) REVERT: B 219 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 235 LYS cc_start: 0.8226 (tmtp) cc_final: 0.7723 (tptt) REVERT: B 269 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7812 (mmtt) REVERT: B 290 ASN cc_start: 0.8136 (p0) cc_final: 0.7679 (p0) REVERT: B 307 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.6251 (mm-30) REVERT: B 316 LYS cc_start: 0.8956 (mttt) cc_final: 0.8198 (pttm) REVERT: B 317 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8486 (tptp) REVERT: B 320 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 327 ASN cc_start: 0.8386 (m-40) cc_final: 0.7949 (m-40) REVERT: B 330 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7983 (tptp) outliers start: 27 outliers final: 22 residues processed: 205 average time/residue: 0.1132 time to fit residues: 29.2683 Evaluate side-chains 215 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 311 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 431 GLN B 20 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109499 restraints weight = 12166.292| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.89 r_work: 0.3273 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7945 Z= 0.194 Angle : 0.580 8.818 10889 Z= 0.303 Chirality : 0.041 0.184 1260 Planarity : 0.004 0.050 1212 Dihedral : 17.799 108.413 1674 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.83 % Allowed : 27.82 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.30), residues: 829 helix: 0.32 (0.25), residues: 456 sheet: -0.94 (0.61), residues: 74 loop : -1.38 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 149 TYR 0.013 0.002 TYR A 23 PHE 0.026 0.001 PHE A 473 TRP 0.009 0.002 TRP B 329 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7945) covalent geometry : angle 0.58025 (10889) hydrogen bonds : bond 0.06265 ( 350) hydrogen bonds : angle 4.73294 ( 980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7871 (mmt) cc_final: 0.7602 (mmt) REVERT: A 56 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7686 (mt-10) REVERT: A 69 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7142 (ptm-80) REVERT: A 72 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 213 TYR cc_start: 0.7660 (m-80) cc_final: 0.6752 (m-80) REVERT: A 316 LYS cc_start: 0.8573 (ttmm) cc_final: 0.7996 (ttpt) REVERT: A 399 MET cc_start: 0.8518 (tpt) cc_final: 0.8301 (tpt) REVERT: A 401 MET cc_start: 0.8645 (mmm) cc_final: 0.8204 (mmm) REVERT: A 411 TYR cc_start: 0.8166 (t80) cc_final: 0.7855 (t80) REVERT: A 490 MET cc_start: 0.7913 (ptm) cc_final: 0.7445 (ppp) REVERT: B 9 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7658 (mmtm) REVERT: B 10 MET cc_start: 0.7176 (mpm) cc_final: 0.6956 (mpm) REVERT: B 54 LYS cc_start: 0.6542 (mmtt) cc_final: 0.6118 (mmtm) REVERT: B 81 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6898 (mm-30) REVERT: B 124 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7519 (tt) REVERT: B 191 LYS cc_start: 0.7241 (mmmm) cc_final: 0.6874 (mmtm) REVERT: B 219 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 235 LYS cc_start: 0.8259 (tmtp) cc_final: 0.7745 (tptt) REVERT: B 269 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7791 (mmtt) REVERT: B 290 ASN cc_start: 0.8141 (p0) cc_final: 0.7713 (p0) REVERT: B 316 LYS cc_start: 0.8883 (mttt) cc_final: 0.8021 (pttm) REVERT: B 320 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 330 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7987 (tptp) outliers start: 43 outliers final: 27 residues processed: 217 average time/residue: 0.1157 time to fit residues: 31.6939 Evaluate side-chains 218 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104661 restraints weight = 11897.531| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.93 r_work: 0.3269 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7945 Z= 0.200 Angle : 0.558 7.879 10889 Z= 0.291 Chirality : 0.041 0.182 1260 Planarity : 0.004 0.039 1212 Dihedral : 17.589 109.209 1643 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.83 % Allowed : 27.68 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.30), residues: 829 helix: 0.54 (0.25), residues: 456 sheet: -1.29 (0.59), residues: 74 loop : -1.46 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 120 TYR 0.012 0.002 TYR A 23 PHE 0.015 0.001 PHE A 473 TRP 0.011 0.002 TRP A 206 HIS 0.005 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 7945) covalent geometry : angle 0.55760 (10889) hydrogen bonds : bond 0.05515 ( 350) hydrogen bonds : angle 4.32890 ( 980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7885 (mmt) cc_final: 0.7638 (mmt) REVERT: A 56 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7624 (mt-10) REVERT: A 69 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.6948 (ptm-80) REVERT: A 72 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 156 TYR cc_start: 0.8861 (m-80) cc_final: 0.8586 (m-80) REVERT: A 213 TYR cc_start: 0.7584 (m-80) cc_final: 0.6722 (m-80) REVERT: A 215 GLU cc_start: 0.6957 (pm20) cc_final: 0.6082 (pm20) REVERT: A 411 TYR cc_start: 0.8288 (t80) cc_final: 0.7974 (t80) REVERT: A 455 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 490 MET cc_start: 0.7994 (ptm) cc_final: 0.7578 (ppp) REVERT: B 9 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7657 (mmtm) REVERT: B 10 MET cc_start: 0.7272 (mpm) cc_final: 0.7053 (mpm) REVERT: B 54 LYS cc_start: 0.6538 (mmtt) cc_final: 0.6117 (mmtm) REVERT: B 81 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6246 (tt0) REVERT: B 124 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7536 (tt) REVERT: B 219 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7955 (mt-10) REVERT: B 235 LYS cc_start: 0.8236 (tmtp) cc_final: 0.7708 (tptt) REVERT: B 269 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7713 (mmtt) REVERT: B 290 ASN cc_start: 0.8167 (p0) cc_final: 0.7742 (p0) REVERT: B 316 LYS cc_start: 0.8868 (mttt) cc_final: 0.8034 (pttm) REVERT: B 320 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 330 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7946 (tptp) outliers start: 43 outliers final: 32 residues processed: 218 average time/residue: 0.1116 time to fit residues: 30.6440 Evaluate side-chains 226 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105986 restraints weight = 12110.873| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3289 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7945 Z= 0.148 Angle : 0.515 8.544 10889 Z= 0.267 Chirality : 0.039 0.183 1260 Planarity : 0.004 0.040 1212 Dihedral : 17.421 109.057 1641 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.70 % Allowed : 27.95 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.30), residues: 829 helix: 0.79 (0.25), residues: 458 sheet: -1.38 (0.58), residues: 74 loop : -1.41 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 120 TYR 0.012 0.002 TYR A 23 PHE 0.016 0.001 PHE A 473 TRP 0.009 0.001 TRP A 206 HIS 0.004 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7945) covalent geometry : angle 0.51503 (10889) hydrogen bonds : bond 0.04283 ( 350) hydrogen bonds : angle 4.03330 ( 980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7871 (mmt) cc_final: 0.7586 (mmt) REVERT: A 20 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7440 (mm-40) REVERT: A 24 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 56 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7608 (mt-10) REVERT: A 72 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 83 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: A 136 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7803 (tttt) REVERT: A 156 TYR cc_start: 0.8806 (m-80) cc_final: 0.8426 (m-80) REVERT: A 188 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7966 (tt) REVERT: A 204 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8480 (mmtm) REVERT: A 208 GLU cc_start: 0.7931 (mp0) cc_final: 0.7710 (mp0) REVERT: A 213 TYR cc_start: 0.7585 (m-80) cc_final: 0.6840 (m-80) REVERT: A 256 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: A 411 TYR cc_start: 0.8285 (t80) cc_final: 0.7956 (t80) REVERT: A 428 MET cc_start: 0.7855 (mtp) cc_final: 0.7635 (mtp) REVERT: B 9 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7581 (mmtm) REVERT: B 10 MET cc_start: 0.7306 (mpm) cc_final: 0.7071 (mpm) REVERT: B 54 LYS cc_start: 0.6463 (mmtt) cc_final: 0.6025 (mmtm) REVERT: B 81 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6165 (tt0) REVERT: B 124 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7480 (tt) REVERT: B 219 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 235 LYS cc_start: 0.8252 (tmtp) cc_final: 0.7765 (tptt) REVERT: B 256 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7264 (m90) REVERT: B 269 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7738 (mmtt) REVERT: B 290 ASN cc_start: 0.8169 (p0) cc_final: 0.7751 (p0) REVERT: B 316 LYS cc_start: 0.8855 (mttt) cc_final: 0.8073 (pttm) REVERT: B 320 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 330 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8022 (mmmt) outliers start: 42 outliers final: 25 residues processed: 212 average time/residue: 0.1120 time to fit residues: 30.1183 Evaluate side-chains 221 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 256 HIS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105755 restraints weight = 11968.245| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.94 r_work: 0.3287 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7945 Z= 0.156 Angle : 0.527 8.143 10889 Z= 0.271 Chirality : 0.039 0.177 1260 Planarity : 0.004 0.050 1212 Dihedral : 17.423 109.425 1641 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.29 % Allowed : 28.77 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.30), residues: 829 helix: 0.88 (0.25), residues: 458 sheet: -1.41 (0.58), residues: 74 loop : -1.40 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 120 TYR 0.012 0.002 TYR A 23 PHE 0.008 0.001 PHE A 464 TRP 0.021 0.002 TRP B 329 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7945) covalent geometry : angle 0.52710 (10889) hydrogen bonds : bond 0.04278 ( 350) hydrogen bonds : angle 3.98172 ( 980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7866 (mmt) cc_final: 0.7575 (mmt) REVERT: A 20 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7427 (mm-40) REVERT: A 24 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 56 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7588 (mt-10) REVERT: A 72 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 83 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8063 (pt0) REVERT: A 136 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7793 (tttt) REVERT: A 156 TYR cc_start: 0.8801 (m-80) cc_final: 0.8434 (m-80) REVERT: A 188 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7969 (tt) REVERT: A 204 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8447 (mmtm) REVERT: A 208 GLU cc_start: 0.7930 (mp0) cc_final: 0.7561 (mp0) REVERT: A 213 TYR cc_start: 0.7577 (m-80) cc_final: 0.6836 (m-80) REVERT: A 405 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8207 (tpp-160) REVERT: A 411 TYR cc_start: 0.8289 (t80) cc_final: 0.7950 (t80) REVERT: B 9 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7563 (mmtm) REVERT: B 10 MET cc_start: 0.7281 (mpm) cc_final: 0.7050 (mpm) REVERT: B 54 LYS cc_start: 0.6450 (mmtt) cc_final: 0.6132 (mmtt) REVERT: B 81 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 219 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 235 LYS cc_start: 0.8226 (tmtp) cc_final: 0.7731 (tptt) REVERT: B 290 ASN cc_start: 0.8181 (p0) cc_final: 0.7743 (p0) REVERT: B 316 LYS cc_start: 0.8884 (mttt) cc_final: 0.8067 (pttm) REVERT: B 320 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 330 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (mmmt) outliers start: 39 outliers final: 29 residues processed: 207 average time/residue: 0.1106 time to fit residues: 28.9755 Evaluate side-chains 220 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106461 restraints weight = 12024.596| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.95 r_work: 0.3295 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7945 Z= 0.136 Angle : 0.517 8.771 10889 Z= 0.265 Chirality : 0.038 0.179 1260 Planarity : 0.003 0.052 1212 Dihedral : 17.365 109.013 1641 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.43 % Allowed : 28.77 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.30), residues: 829 helix: 1.01 (0.25), residues: 458 sheet: -1.34 (0.58), residues: 74 loop : -1.38 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 120 TYR 0.012 0.001 TYR A 23 PHE 0.011 0.001 PHE B 253 TRP 0.027 0.002 TRP B 329 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7945) covalent geometry : angle 0.51687 (10889) hydrogen bonds : bond 0.03947 ( 350) hydrogen bonds : angle 3.90243 ( 980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7867 (mmt) cc_final: 0.7619 (mmt) REVERT: A 20 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7381 (mm-40) REVERT: A 24 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8460 (p) REVERT: A 56 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7580 (mt-10) REVERT: A 72 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 83 GLU cc_start: 0.8324 (pt0) cc_final: 0.8096 (pt0) REVERT: A 136 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (tttt) REVERT: A 156 TYR cc_start: 0.8780 (m-80) cc_final: 0.8315 (m-80) REVERT: A 188 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 204 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8439 (mmtm) REVERT: A 208 GLU cc_start: 0.7931 (mp0) cc_final: 0.7704 (mp0) REVERT: A 213 TYR cc_start: 0.7566 (m-80) cc_final: 0.6837 (m-80) REVERT: A 256 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: A 370 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7830 (mtm180) REVERT: A 405 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8312 (tpp-160) REVERT: A 411 TYR cc_start: 0.8280 (t80) cc_final: 0.7937 (t80) REVERT: A 458 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.8018 (m110) REVERT: B 9 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7544 (mmtm) REVERT: B 10 MET cc_start: 0.7285 (mpm) cc_final: 0.7054 (mpm) REVERT: B 44 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 54 LYS cc_start: 0.6480 (mmtt) cc_final: 0.6021 (mmtm) REVERT: B 81 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6732 (mm-30) REVERT: B 216 LYS cc_start: 0.8847 (tmmt) cc_final: 0.8460 (tmmt) REVERT: B 219 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7936 (mt-10) REVERT: B 222 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: B 235 LYS cc_start: 0.8231 (tmtp) cc_final: 0.7748 (tptt) REVERT: B 290 ASN cc_start: 0.8166 (p0) cc_final: 0.7720 (p0) REVERT: B 316 LYS cc_start: 0.8865 (mttt) cc_final: 0.8076 (pttm) REVERT: B 320 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 330 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7995 (mmmt) outliers start: 40 outliers final: 28 residues processed: 208 average time/residue: 0.1103 time to fit residues: 29.2409 Evaluate side-chains 219 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105447 restraints weight = 11929.888| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.94 r_work: 0.3281 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7945 Z= 0.170 Angle : 0.539 8.331 10889 Z= 0.277 Chirality : 0.040 0.190 1260 Planarity : 0.004 0.062 1212 Dihedral : 17.270 108.182 1641 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.43 % Allowed : 28.63 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.30), residues: 829 helix: 1.01 (0.25), residues: 458 sheet: -1.39 (0.58), residues: 74 loop : -1.41 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 120 TYR 0.012 0.002 TYR A 23 PHE 0.018 0.001 PHE B 253 TRP 0.025 0.002 TRP B 329 HIS 0.004 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7945) covalent geometry : angle 0.53886 (10889) hydrogen bonds : bond 0.04346 ( 350) hydrogen bonds : angle 3.94333 ( 980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: A 24 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 56 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7611 (mt-10) REVERT: A 83 GLU cc_start: 0.8338 (pt0) cc_final: 0.8115 (pt0) REVERT: A 136 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7832 (tttt) REVERT: A 156 TYR cc_start: 0.8786 (m-80) cc_final: 0.8377 (m-80) REVERT: A 188 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 204 LYS cc_start: 0.8685 (mmtp) cc_final: 0.8448 (mmtm) REVERT: A 213 TYR cc_start: 0.7603 (m-80) cc_final: 0.6854 (m-80) REVERT: A 256 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: B 9 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7605 (mmtm) REVERT: B 10 MET cc_start: 0.7336 (mpm) cc_final: 0.7100 (mpm) REVERT: B 44 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6735 (tm-30) REVERT: B 54 LYS cc_start: 0.6539 (mmtt) cc_final: 0.6197 (mmtt) REVERT: B 81 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6178 (tt0) REVERT: B 161 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.5898 (tp) REVERT: B 216 LYS cc_start: 0.8847 (tmmt) cc_final: 0.8465 (tmmt) REVERT: B 219 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 222 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: B 235 LYS cc_start: 0.8243 (tmtp) cc_final: 0.7752 (tptt) REVERT: B 290 ASN cc_start: 0.8183 (p0) cc_final: 0.7725 (p0) REVERT: B 316 LYS cc_start: 0.8861 (mttt) cc_final: 0.8086 (pttm) REVERT: B 320 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7575 (mm-30) REVERT: B 330 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8003 (mmmt) outliers start: 40 outliers final: 27 residues processed: 204 average time/residue: 0.1161 time to fit residues: 29.9466 Evaluate side-chains 216 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105659 restraints weight = 12159.883| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.95 r_work: 0.3284 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7945 Z= 0.167 Angle : 0.551 9.348 10889 Z= 0.281 Chirality : 0.040 0.190 1260 Planarity : 0.004 0.066 1212 Dihedral : 17.178 107.386 1639 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.16 % Allowed : 29.31 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.30), residues: 829 helix: 1.05 (0.26), residues: 458 sheet: -1.38 (0.58), residues: 74 loop : -1.41 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 120 TYR 0.013 0.002 TYR A 23 PHE 0.007 0.001 PHE A 464 TRP 0.025 0.002 TRP B 329 HIS 0.004 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7945) covalent geometry : angle 0.55083 (10889) hydrogen bonds : bond 0.04202 ( 350) hydrogen bonds : angle 3.91902 ( 980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7314 (mm-40) REVERT: A 24 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 56 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7619 (mt-10) REVERT: A 72 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 83 GLU cc_start: 0.8357 (pt0) cc_final: 0.8124 (pt0) REVERT: A 136 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7836 (tttt) REVERT: A 156 TYR cc_start: 0.8799 (m-80) cc_final: 0.8395 (m-80) REVERT: A 188 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 204 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8443 (mmtm) REVERT: A 213 TYR cc_start: 0.7591 (m-80) cc_final: 0.6851 (m-80) REVERT: A 256 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: A 370 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7890 (mtm180) REVERT: A 405 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8290 (tpp-160) REVERT: A 411 TYR cc_start: 0.8276 (t80) cc_final: 0.7992 (t80) REVERT: A 458 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.8002 (m110) REVERT: B 10 MET cc_start: 0.7348 (mpm) cc_final: 0.7098 (mpm) REVERT: B 44 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6814 (tm-30) REVERT: B 54 LYS cc_start: 0.6424 (mmtt) cc_final: 0.6087 (mmtm) REVERT: B 81 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 161 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.5904 (tp) REVERT: B 216 LYS cc_start: 0.8840 (tmmt) cc_final: 0.8456 (tmmt) REVERT: B 222 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: B 235 LYS cc_start: 0.8246 (tmtp) cc_final: 0.7754 (tptt) REVERT: B 290 ASN cc_start: 0.8164 (p0) cc_final: 0.7690 (p0) REVERT: B 316 LYS cc_start: 0.8865 (mttt) cc_final: 0.8080 (pttm) REVERT: B 330 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8003 (mmmt) outliers start: 38 outliers final: 29 residues processed: 203 average time/residue: 0.1200 time to fit residues: 30.8058 Evaluate side-chains 222 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 330 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 43 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.132262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108248 restraints weight = 12153.749| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.93 r_work: 0.3330 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7945 Z= 0.106 Angle : 0.534 10.222 10889 Z= 0.270 Chirality : 0.038 0.183 1260 Planarity : 0.003 0.061 1212 Dihedral : 17.059 105.074 1639 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.80 % Allowed : 31.21 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.31), residues: 829 helix: 1.23 (0.26), residues: 459 sheet: -1.23 (0.60), residues: 74 loop : -1.33 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 120 TYR 0.015 0.001 TYR A 23 PHE 0.007 0.001 PHE A 464 TRP 0.022 0.001 TRP B 329 HIS 0.002 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7945) covalent geometry : angle 0.53403 (10889) hydrogen bonds : bond 0.03382 ( 350) hydrogen bonds : angle 3.76182 ( 980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7547 (mt-10) REVERT: A 69 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.6982 (ptm-80) REVERT: A 72 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 83 GLU cc_start: 0.8350 (pt0) cc_final: 0.8124 (pt0) REVERT: A 136 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7815 (tttt) REVERT: A 156 TYR cc_start: 0.8761 (m-80) cc_final: 0.8283 (m-80) REVERT: A 204 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8508 (mmtm) REVERT: A 213 TYR cc_start: 0.7528 (m-80) cc_final: 0.6869 (m-80) REVERT: A 218 LEU cc_start: 0.7304 (mm) cc_final: 0.6995 (mm) REVERT: A 256 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: A 370 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7844 (mtm180) REVERT: A 401 MET cc_start: 0.8580 (mmm) cc_final: 0.7934 (mmm) REVERT: A 405 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8322 (ttm110) REVERT: A 411 TYR cc_start: 0.8299 (t80) cc_final: 0.8010 (t80) REVERT: B 10 MET cc_start: 0.7299 (mpm) cc_final: 0.7042 (mpm) REVERT: B 44 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6808 (tm-30) REVERT: B 54 LYS cc_start: 0.6490 (mmtt) cc_final: 0.6206 (mmtt) REVERT: B 81 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6118 (tt0) REVERT: B 216 LYS cc_start: 0.8793 (tmmt) cc_final: 0.8418 (tmmt) REVERT: B 222 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: B 235 LYS cc_start: 0.8237 (tmtp) cc_final: 0.7762 (tptt) REVERT: B 290 ASN cc_start: 0.8133 (p0) cc_final: 0.7638 (p0) REVERT: B 316 LYS cc_start: 0.8593 (mttt) cc_final: 0.8373 (pttm) REVERT: B 330 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8025 (mmmt) outliers start: 28 outliers final: 21 residues processed: 198 average time/residue: 0.1155 time to fit residues: 28.7207 Evaluate side-chains 208 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 458 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109336 restraints weight = 12211.791| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.88 r_work: 0.3290 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7945 Z= 0.179 Angle : 0.582 13.514 10889 Z= 0.294 Chirality : 0.041 0.201 1260 Planarity : 0.004 0.075 1212 Dihedral : 17.010 105.165 1632 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.80 % Allowed : 31.34 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.31), residues: 829 helix: 1.13 (0.26), residues: 459 sheet: -1.36 (0.59), residues: 74 loop : -1.39 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 120 TYR 0.012 0.002 TYR A 23 PHE 0.009 0.001 PHE B 184 TRP 0.023 0.002 TRP B 329 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7945) covalent geometry : angle 0.58204 (10889) hydrogen bonds : bond 0.04263 ( 350) hydrogen bonds : angle 3.92166 ( 980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7639 (mt-10) REVERT: A 72 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 136 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7826 (tttt) REVERT: A 156 TYR cc_start: 0.8799 (m-80) cc_final: 0.8440 (m-80) REVERT: A 213 TYR cc_start: 0.7609 (m-80) cc_final: 0.6872 (m-80) REVERT: A 218 LEU cc_start: 0.7369 (mm) cc_final: 0.7057 (mm) REVERT: A 256 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: A 370 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7837 (mtm180) REVERT: A 405 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8087 (ttm170) REVERT: B 10 MET cc_start: 0.7325 (mpm) cc_final: 0.7084 (mpm) REVERT: B 44 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6852 (tm-30) REVERT: B 54 LYS cc_start: 0.6430 (mmtt) cc_final: 0.6038 (mmtm) REVERT: B 81 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6167 (tt0) REVERT: B 216 LYS cc_start: 0.8794 (tmmt) cc_final: 0.8440 (tmmt) REVERT: B 222 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: B 235 LYS cc_start: 0.8260 (tmtp) cc_final: 0.7772 (tptt) REVERT: B 290 ASN cc_start: 0.8109 (p0) cc_final: 0.7613 (p0) REVERT: B 330 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8079 (mmmt) outliers start: 28 outliers final: 23 residues processed: 196 average time/residue: 0.1197 time to fit residues: 29.3117 Evaluate side-chains 205 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 8 MET Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109863 restraints weight = 12204.580| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.87 r_work: 0.3297 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7945 Z= 0.166 Angle : 0.584 13.359 10889 Z= 0.293 Chirality : 0.040 0.197 1260 Planarity : 0.004 0.072 1212 Dihedral : 16.987 105.588 1632 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.93 % Allowed : 31.48 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.30), residues: 829 helix: 1.14 (0.25), residues: 459 sheet: -1.44 (0.59), residues: 74 loop : -1.38 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 120 TYR 0.013 0.002 TYR A 23 PHE 0.015 0.001 PHE B 253 TRP 0.022 0.002 TRP B 329 HIS 0.003 0.001 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 7945) covalent geometry : angle 0.58402 (10889) hydrogen bonds : bond 0.03884 ( 350) hydrogen bonds : angle 3.89125 ( 980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.99 seconds wall clock time: 40 minutes 55.92 seconds (2455.92 seconds total)