Starting phenix.real_space_refine on Fri Aug 22 18:34:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.map" model { file = "/net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij5_35465/08_2025/8ij5_35465.cif" } resolution = 3.0 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4314 2.51 5 N 1144 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6815 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2804 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Chain: "E" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4011 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 4 Time building chain proxies: 1.33, per 1000 atoms: 0.20 Number of scatterers: 6815 At special positions: 0 Unit cell: (68.64, 104.28, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1321 8.00 N 1144 7.00 C 4314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 258 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 158 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 185 " distance=2.03 Simple disulfide: pdb=" SG CYS E 508 " - pdb=" SG CYS E 565 " distance=2.04 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: 0.36 Conformation dependent library (CDL) restraints added in 232.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 18 sheets defined 11.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 150 through 157 removed outlier: 3.596A pdb=" N TRP B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.505A pdb=" N TYR B 190 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.097A pdb=" N PHE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Processing helix chain 'B' and resid 319 through 328 removed outlier: 3.526A pdb=" N GLN B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 365 through 378 Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 244 through 248 Processing sheet with id=AA1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.876A pdb=" N LYS B 124 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.876A pdb=" N LYS B 124 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 426 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 223 removed outlier: 6.405A pdb=" N PHE B 179 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR B 221 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE B 177 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 223 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 175 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP B 139 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 273 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 141 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR B 275 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU B 143 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 276 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 332 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY B 357 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE B 334 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 411 through 413 removed outlier: 3.617A pdb=" N VAL B 381 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.419A pdb=" N ASP E 451 " --> pdb=" O ALA E 441 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 441 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER E 437 " --> pdb=" O GLY E 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.703A pdb=" N HIS E 143 " --> pdb=" O PHE E 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 127 through 131 removed outlier: 4.107A pdb=" N SER E 127 " --> pdb=" O CYS E 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 190 through 192 Processing sheet with id=AB2, first strand: chain 'E' and resid 256 through 259 Processing sheet with id=AB3, first strand: chain 'E' and resid 310 through 313 Processing sheet with id=AB4, first strand: chain 'E' and resid 331 through 333 Processing sheet with id=AB5, first strand: chain 'E' and resid 374 through 378 removed outlier: 6.299A pdb=" N ILE E 374 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA E 391 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA E 389 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 378 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 374 through 378 removed outlier: 6.299A pdb=" N ILE E 374 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA E 391 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA E 389 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 378 " --> pdb=" O ASP E 387 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 419 " --> pdb=" O ILE E 405 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 564 through 568 removed outlier: 3.608A pdb=" N GLN E 564 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU E 566 " --> pdb=" O PHE E 507 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'E' and resid 525 through 528 removed outlier: 3.697A pdb=" N GLU E 526 " --> pdb=" O GLU E 590 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 590 " --> pdb=" O GLU E 526 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2257 1.34 - 1.46: 1601 1.46 - 1.59: 3037 1.59 - 1.71: 0 1.71 - 1.83: 57 Bond restraints: 6952 Sorted by residual: bond pdb=" N MET E 148 " pdb=" CA MET E 148 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.52e+00 bond pdb=" N GLU E 117 " pdb=" CA GLU E 117 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.25e-02 6.40e+03 4.69e+00 bond pdb=" N GLU E 147 " pdb=" CA GLU E 147 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.27e-02 6.20e+03 4.66e+00 bond pdb=" N TYR E 142 " pdb=" CA TYR E 142 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.23e-02 6.61e+03 4.46e+00 bond pdb=" C VAL E 416 " pdb=" N PRO E 417 " ideal model delta sigma weight residual 1.331 1.355 -0.025 1.31e-02 5.83e+03 3.64e+00 ... (remaining 6947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 9254 2.08 - 4.16: 133 4.16 - 6.24: 17 6.24 - 8.32: 4 8.32 - 10.40: 1 Bond angle restraints: 9409 Sorted by residual: angle pdb=" C VAL E 459 " pdb=" N ASP E 460 " pdb=" CA ASP E 460 " ideal model delta sigma weight residual 121.54 127.85 -6.31 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N VAL E 342 " pdb=" CA VAL E 342 " pdb=" C VAL E 342 " ideal model delta sigma weight residual 113.71 110.61 3.10 9.50e-01 1.11e+00 1.06e+01 angle pdb=" N MET E 148 " pdb=" CA MET E 148 " pdb=" C MET E 148 " ideal model delta sigma weight residual 110.80 103.87 6.93 2.13e+00 2.20e-01 1.06e+01 angle pdb=" CA GLU E 147 " pdb=" C GLU E 147 " pdb=" O GLU E 147 " ideal model delta sigma weight residual 120.98 117.73 3.25 1.08e+00 8.57e-01 9.08e+00 angle pdb=" CA LEU B 90 " pdb=" CB LEU B 90 " pdb=" CG LEU B 90 " ideal model delta sigma weight residual 116.30 126.70 -10.40 3.50e+00 8.16e-02 8.82e+00 ... (remaining 9404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3400 17.70 - 35.41: 518 35.41 - 53.11: 199 53.11 - 70.81: 45 70.81 - 88.51: 8 Dihedral angle restraints: 4170 sinusoidal: 1661 harmonic: 2509 Sorted by residual: dihedral pdb=" CB CYS E 172 " pdb=" SG CYS E 172 " pdb=" SG CYS E 185 " pdb=" CB CYS E 185 " ideal model delta sinusoidal sigma weight residual 93.00 55.84 37.16 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA CYS B 258 " pdb=" CB CYS B 258 " pdb=" SG CYS B 258 " pdb=" SG CYS B 299 " ideal model delta sinusoidal sigma weight residual -73.00 -5.09 -67.91 1 2.00e+01 2.50e-03 1.50e+01 dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N ARG B 119 " pdb=" CA ARG B 119 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 769 0.048 - 0.095: 201 0.095 - 0.143: 62 0.143 - 0.191: 0 0.191 - 0.239: 1 Chirality restraints: 1033 Sorted by residual: chirality pdb=" CA MET E 148 " pdb=" N MET E 148 " pdb=" C MET E 148 " pdb=" CB MET E 148 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP E 460 " pdb=" N ASP E 460 " pdb=" C ASP E 460 " pdb=" CB ASP E 460 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 425 " pdb=" N ILE B 425 " pdb=" C ILE B 425 " pdb=" CB ILE B 425 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1030 not shown) Planarity restraints: 1237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 57 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO E 58 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 58 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 58 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 57 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C VAL E 57 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL E 57 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO E 58 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 430 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO E 431 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 431 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 431 " -0.024 5.00e-02 4.00e+02 ... (remaining 1234 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1185 2.77 - 3.30: 6128 3.30 - 3.83: 11319 3.83 - 4.37: 13529 4.37 - 4.90: 23444 Nonbonded interactions: 55605 Sorted by model distance: nonbonded pdb=" N GLY E 334 " pdb=" O LYS E 338 " model vdw 2.234 3.120 nonbonded pdb=" O MET B 191 " pdb=" NH2 ARG B 242 " model vdw 2.259 3.120 nonbonded pdb=" O LEU B 211 " pdb=" OG SER B 239 " model vdw 2.263 3.040 nonbonded pdb=" N ASP B 139 " pdb=" OD1 ASP B 139 " model vdw 2.298 3.120 nonbonded pdb=" O LEU E 116 " pdb=" N ARG E 145 " model vdw 2.324 3.120 ... (remaining 55600 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: 2.060 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.940 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:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 0.040 6959 Z= 0.147 Angle : 0.616 10.395 9423 Z= 0.330 Chirality : 0.045 0.239 1033 Planarity : 0.004 0.060 1237 Dihedral : 19.835 88.512 2545 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.07 % Favored : 90.81 % Rotamer: Outliers : 11.22 % Allowed : 34.19 % Favored : 54.59 % 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 aren not related in a simple way. whole: -2.39 (0.27), residues: 860 helix: -1.39 (0.54), residues: 80 sheet: -0.58 (0.33), residues: 275 loop : -2.31 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 95 TYR 0.016 0.001 TYR B 136 PHE 0.014 0.001 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6952) covalent geometry : angle 0.61499 ( 9409) SS BOND : bond 0.00345 ( 7) SS BOND : angle 1.24379 ( 14) hydrogen bonds : bond 0.25941 ( 192) hydrogen bonds : angle 10.18415 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 171 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: B 146 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6762 (mt) REVERT: B 386 ARG cc_start: 0.6486 (mtt90) cc_final: 0.6052 (mtt90) outliers start: 83 outliers final: 75 residues processed: 243 average time/residue: 0.3957 time to fit residues: 102.1409 Evaluate side-chains 243 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 ARG Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 369 ARG Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 526 GLU Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 558 SER Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 564 GLN Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 590 GLU Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 615 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN B 346 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114944 restraints weight = 10022.129| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.63 r_work: 0.3412 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6959 Z= 0.236 Angle : 0.682 7.742 9423 Z= 0.361 Chirality : 0.048 0.167 1033 Planarity : 0.005 0.052 1237 Dihedral : 12.585 76.505 1079 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.58 % Favored : 89.30 % Rotamer: Outliers : 10.68 % Allowed : 32.30 % Favored : 57.03 % 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 aren not related in a simple way. whole: -2.31 (0.28), residues: 860 helix: -1.24 (0.53), residues: 89 sheet: -0.50 (0.32), residues: 283 loop : -2.32 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 242 TYR 0.016 0.002 TYR B 347 PHE 0.031 0.002 PHE B 440 TRP 0.008 0.001 TRP E 144 HIS 0.005 0.002 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 6952) covalent geometry : angle 0.68202 ( 9409) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.88042 ( 14) hydrogen bonds : bond 0.04987 ( 192) hydrogen bonds : angle 7.37912 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 174 time to evaluate : 0.267 Fit side-chains REVERT: B 146 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7195 (mt) REVERT: B 384 GLU cc_start: 0.7370 (pp20) cc_final: 0.7033 (pp20) REVERT: E 216 ASP cc_start: 0.7324 (m-30) cc_final: 0.7084 (m-30) REVERT: E 445 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: E 460 ASP cc_start: 0.7600 (p0) cc_final: 0.7385 (p0) outliers start: 79 outliers final: 57 residues processed: 231 average time/residue: 0.3881 time to fit residues: 95.4952 Evaluate side-chains 228 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.0070 chunk 18 optimal weight: 0.0070 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116833 restraints weight = 9973.071| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.62 r_work: 0.3440 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6959 Z= 0.134 Angle : 0.607 9.106 9423 Z= 0.321 Chirality : 0.045 0.168 1033 Planarity : 0.005 0.051 1237 Dihedral : 9.758 59.989 1011 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 9.46 % Allowed : 34.19 % Favored : 56.35 % 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 aren not related in a simple way. whole: -2.15 (0.28), residues: 860 helix: -1.00 (0.54), residues: 89 sheet: -0.43 (0.32), residues: 282 loop : -2.21 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.015 0.001 TYR B 136 PHE 0.024 0.001 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6952) covalent geometry : angle 0.60636 ( 9409) SS BOND : bond 0.00256 ( 7) SS BOND : angle 1.07392 ( 14) hydrogen bonds : bond 0.04088 ( 192) hydrogen bonds : angle 6.88496 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 0.196 Fit side-chains REVERT: B 216 TYR cc_start: 0.8308 (t80) cc_final: 0.8096 (t80) REVERT: B 287 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8119 (ptm-80) REVERT: B 384 GLU cc_start: 0.7374 (pp20) cc_final: 0.7094 (pp20) REVERT: E 145 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (tmt-80) REVERT: E 216 ASP cc_start: 0.7307 (m-30) cc_final: 0.7065 (m-30) REVERT: E 331 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: E 460 ASP cc_start: 0.7721 (p0) cc_final: 0.7515 (p0) outliers start: 70 outliers final: 46 residues processed: 229 average time/residue: 0.3886 time to fit residues: 94.7338 Evaluate side-chains 217 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 144 TRP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 83 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115233 restraints weight = 10045.800| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.63 r_work: 0.3415 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6959 Z= 0.214 Angle : 0.661 7.263 9423 Z= 0.349 Chirality : 0.048 0.162 1033 Planarity : 0.005 0.050 1237 Dihedral : 9.250 59.624 994 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 10.00 % Allowed : 33.78 % Favored : 56.22 % 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 aren not related in a simple way. whole: -2.20 (0.28), residues: 860 helix: -1.12 (0.52), residues: 90 sheet: -0.37 (0.33), residues: 280 loop : -2.29 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 378 TYR 0.011 0.002 TYR E 449 PHE 0.024 0.002 PHE B 440 TRP 0.009 0.001 TRP E 144 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 6952) covalent geometry : angle 0.65704 ( 9409) SS BOND : bond 0.00369 ( 7) SS BOND : angle 1.97109 ( 14) hydrogen bonds : bond 0.04265 ( 192) hydrogen bonds : angle 6.74413 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 0.257 Fit side-chains REVERT: B 287 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8147 (ptm-80) REVERT: B 384 GLU cc_start: 0.7424 (pp20) cc_final: 0.7104 (pp20) REVERT: E 145 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7662 (tmt-80) REVERT: E 216 ASP cc_start: 0.7394 (m-30) cc_final: 0.7133 (m-30) REVERT: E 305 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6078 (m-80) REVERT: E 365 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7777 (mt-10) REVERT: E 445 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.4594 (m-30) outliers start: 74 outliers final: 47 residues processed: 223 average time/residue: 0.4305 time to fit residues: 102.1815 Evaluate side-chains 214 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 163 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 145 ARG Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.3980 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116017 restraints weight = 10033.861| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.62 r_work: 0.3429 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6959 Z= 0.180 Angle : 0.649 9.531 9423 Z= 0.341 Chirality : 0.047 0.161 1033 Planarity : 0.005 0.051 1237 Dihedral : 8.966 58.852 990 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.12 % Favored : 89.77 % Rotamer: Outliers : 9.73 % Allowed : 34.32 % Favored : 55.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.28), residues: 860 helix: -0.96 (0.53), residues: 90 sheet: -0.36 (0.33), residues: 279 loop : -2.24 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 378 TYR 0.015 0.002 TYR B 136 PHE 0.021 0.002 PHE B 440 TRP 0.007 0.001 TRP E 209 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6952) covalent geometry : angle 0.64492 ( 9409) SS BOND : bond 0.00510 ( 7) SS BOND : angle 1.93703 ( 14) hydrogen bonds : bond 0.03981 ( 192) hydrogen bonds : angle 6.57547 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 0.286 Fit side-chains REVERT: B 287 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8155 (ptm-80) REVERT: B 384 GLU cc_start: 0.7443 (pp20) cc_final: 0.7138 (pp20) REVERT: E 216 ASP cc_start: 0.7318 (m-30) cc_final: 0.7092 (m-30) REVERT: E 305 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.6083 (m-80) outliers start: 72 outliers final: 55 residues processed: 221 average time/residue: 0.4625 time to fit residues: 108.6890 Evaluate side-chains 220 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 0.0470 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117460 restraints weight = 10039.176| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.63 r_work: 0.3453 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6959 Z= 0.131 Angle : 0.610 9.004 9423 Z= 0.320 Chirality : 0.045 0.160 1033 Planarity : 0.005 0.051 1237 Dihedral : 8.541 58.591 990 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.07 % Favored : 90.81 % Rotamer: Outliers : 8.92 % Allowed : 35.00 % Favored : 56.08 % 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 aren not related in a simple way. whole: -2.02 (0.28), residues: 860 helix: -0.70 (0.54), residues: 90 sheet: -0.33 (0.33), residues: 282 loop : -2.18 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 378 TYR 0.016 0.001 TYR B 136 PHE 0.016 0.001 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6952) covalent geometry : angle 0.60738 ( 9409) SS BOND : bond 0.00392 ( 7) SS BOND : angle 1.53096 ( 14) hydrogen bonds : bond 0.03576 ( 192) hydrogen bonds : angle 6.34929 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 168 time to evaluate : 0.225 Fit side-chains REVERT: B 287 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8122 (ptm-80) REVERT: B 384 GLU cc_start: 0.7407 (pp20) cc_final: 0.7109 (pp20) REVERT: E 305 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: E 331 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8242 (mtm) REVERT: E 365 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7820 (mt-10) outliers start: 66 outliers final: 42 residues processed: 215 average time/residue: 0.3916 time to fit residues: 89.3756 Evaluate side-chains 211 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 63 optimal weight: 0.9980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 158 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116746 restraints weight = 9942.820| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.64 r_work: 0.3441 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6959 Z= 0.156 Angle : 0.621 8.194 9423 Z= 0.327 Chirality : 0.046 0.162 1033 Planarity : 0.005 0.049 1237 Dihedral : 8.422 59.271 981 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.00 % Favored : 89.88 % Rotamer: Outliers : 8.38 % Allowed : 35.54 % Favored : 56.08 % 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 aren not related in a simple way. whole: -2.03 (0.28), residues: 860 helix: -0.70 (0.53), residues: 90 sheet: -0.35 (0.33), residues: 281 loop : -2.17 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 378 TYR 0.013 0.001 TYR B 142 PHE 0.019 0.002 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6952) covalent geometry : angle 0.61872 ( 9409) SS BOND : bond 0.00476 ( 7) SS BOND : angle 1.59321 ( 14) hydrogen bonds : bond 0.03653 ( 192) hydrogen bonds : angle 6.32525 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.242 Fit side-chains REVERT: B 287 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8132 (ptm-80) REVERT: B 384 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: E 305 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6079 (m-80) REVERT: E 365 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7838 (mt-10) outliers start: 62 outliers final: 52 residues processed: 208 average time/residue: 0.4273 time to fit residues: 94.5136 Evaluate side-chains 221 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 54 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 29 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.2508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 298 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117353 restraints weight = 10055.284| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.66 r_work: 0.3449 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6959 Z= 0.137 Angle : 0.610 8.111 9423 Z= 0.322 Chirality : 0.046 0.189 1033 Planarity : 0.005 0.049 1237 Dihedral : 8.138 58.476 979 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 8.51 % Allowed : 35.00 % Favored : 56.49 % 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 aren not related in a simple way. whole: -1.99 (0.28), residues: 860 helix: -0.65 (0.54), residues: 91 sheet: -0.37 (0.33), residues: 283 loop : -2.12 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 378 TYR 0.014 0.001 TYR B 142 PHE 0.017 0.001 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6952) covalent geometry : angle 0.60763 ( 9409) SS BOND : bond 0.00441 ( 7) SS BOND : angle 1.47912 ( 14) hydrogen bonds : bond 0.03515 ( 192) hydrogen bonds : angle 6.26325 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 0.271 Fit side-chains REVERT: B 287 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8128 (ptm-80) REVERT: B 384 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7105 (pp20) REVERT: E 305 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: E 365 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7832 (mt-10) outliers start: 63 outliers final: 50 residues processed: 211 average time/residue: 0.5005 time to fit residues: 111.9086 Evaluate side-chains 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 407 ASN Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 604 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 0.0870 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 158 GLN B 298 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116422 restraints weight = 10019.996| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.61 r_work: 0.3433 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6959 Z= 0.186 Angle : 0.655 8.362 9423 Z= 0.343 Chirality : 0.047 0.175 1033 Planarity : 0.005 0.053 1237 Dihedral : 8.144 58.654 977 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 8.11 % Allowed : 36.08 % Favored : 55.81 % 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 aren not related in a simple way. whole: -2.01 (0.28), residues: 860 helix: -0.70 (0.53), residues: 91 sheet: -0.37 (0.33), residues: 281 loop : -2.14 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 131 TYR 0.016 0.002 TYR B 142 PHE 0.020 0.002 PHE B 440 TRP 0.007 0.001 TRP E 144 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6952) covalent geometry : angle 0.65230 ( 9409) SS BOND : bond 0.00482 ( 7) SS BOND : angle 1.62411 ( 14) hydrogen bonds : bond 0.03724 ( 192) hydrogen bonds : angle 6.31526 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.281 Fit side-chains REVERT: B 287 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8165 (ptm-80) REVERT: B 384 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7118 (pp20) REVERT: E 148 MET cc_start: 0.7958 (ttm) cc_final: 0.7608 (ttm) REVERT: E 305 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: E 474 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7707 (m110) outliers start: 60 outliers final: 54 residues processed: 209 average time/residue: 0.4506 time to fit residues: 99.7213 Evaluate side-chains 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 161 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 0.0270 chunk 64 optimal weight: 0.0770 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116903 restraints weight = 10080.192| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.63 r_work: 0.3441 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6959 Z= 0.159 Angle : 0.655 11.247 9423 Z= 0.339 Chirality : 0.047 0.169 1033 Planarity : 0.005 0.050 1237 Dihedral : 7.993 58.643 977 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 7.84 % Allowed : 36.62 % Favored : 55.54 % 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 aren not related in a simple way. whole: -1.99 (0.28), residues: 860 helix: -0.70 (0.53), residues: 92 sheet: -0.35 (0.33), residues: 281 loop : -2.11 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 131 TYR 0.018 0.001 TYR B 136 PHE 0.018 0.002 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6952) covalent geometry : angle 0.65184 ( 9409) SS BOND : bond 0.00456 ( 7) SS BOND : angle 1.66712 ( 14) hydrogen bonds : bond 0.03608 ( 192) hydrogen bonds : angle 6.28760 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 163 time to evaluate : 0.272 Fit side-chains REVERT: B 158 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7268 (tp-100) REVERT: B 282 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (pt) REVERT: B 287 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8163 (ptm-80) REVERT: B 384 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: E 148 MET cc_start: 0.7912 (ttm) cc_final: 0.7575 (ttm) REVERT: E 305 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.6114 (m-80) outliers start: 58 outliers final: 51 residues processed: 205 average time/residue: 0.4208 time to fit residues: 91.7980 Evaluate side-chains 216 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 301 GLN Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 601 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 0.0170 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 43 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 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 = 0.3650 r_free = 0.3650 target = 0.126281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117125 restraints weight = 9938.531| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.62 r_work: 0.3445 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6959 Z= 0.159 Angle : 0.654 11.192 9423 Z= 0.340 Chirality : 0.047 0.172 1033 Planarity : 0.005 0.049 1237 Dihedral : 7.704 58.668 974 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 7.70 % Allowed : 36.49 % Favored : 55.81 % 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 aren not related in a simple way. whole: -2.03 (0.29), residues: 860 helix: -0.74 (0.52), residues: 92 sheet: -0.42 (0.33), residues: 283 loop : -2.12 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 131 TYR 0.017 0.001 TYR B 136 PHE 0.017 0.002 PHE B 440 TRP 0.007 0.001 TRP B 264 HIS 0.005 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6952) covalent geometry : angle 0.65159 ( 9409) SS BOND : bond 0.00453 ( 7) SS BOND : angle 1.63793 ( 14) hydrogen bonds : bond 0.03597 ( 192) hydrogen bonds : angle 6.36490 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.88 seconds wall clock time: 42 minutes 46.18 seconds (2566.18 seconds total)