Starting phenix.real_space_refine on Sat May 10 20:51:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij5_35465/05_2025/8ij5_35465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij5_35465/05_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_35465/05_2025/8ij5_35465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij5_35465/05_2025/8ij5_35465.map" model { file = "/net/cci-nas-00/data/ceres_data/8ij5_35465/05_2025/8ij5_35465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij5_35465/05_2025/8ij5_35465.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.64, per 1000 atoms: 0.68 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: 1.53 Conformation dependent library (CDL) restraints added in 954.7 milliseconds 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: 0.91 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: 2.11 Time building geometry restraints manager: 1.82 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.420 ------------------------------------------------------------------------------- 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 : 10.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (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 TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS B 218 PHE 0.014 0.001 PHE B 440 TYR 0.016 0.001 TYR B 136 ARG 0.007 0.000 ARG E 95 Details of bonding type rmsd hydrogen bonds : bond 0.25941 ( 192) hydrogen bonds : angle 10.18415 ( 507) SS BOND : bond 0.00345 ( 7) SS BOND : angle 1.24379 ( 14) covalent geometry : bond 0.00315 ( 6952) covalent geometry : angle 0.61499 ( 9409) *********************** 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 : 0.803 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: 0.9776 time to fit residues: 252.2745 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 : 0.741 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.0040 chunk 41 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.2750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** 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 = 0.3649 r_free = 0.3649 target = 0.126232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117099 restraints weight = 9898.537| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.62 r_work: 0.3444 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6959 Z= 0.145 Angle : 0.620 8.359 9423 Z= 0.328 Chirality : 0.045 0.164 1033 Planarity : 0.005 0.052 1237 Dihedral : 12.200 75.249 1079 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.19 % Favored : 90.70 % Rotamer: Outliers : 8.24 % Allowed : 34.59 % Favored : 57.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.28), residues: 860 helix: -1.03 (0.54), residues: 89 sheet: -0.48 (0.32), residues: 287 loop : -2.17 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 264 HIS 0.004 0.001 HIS B 218 PHE 0.028 0.001 PHE B 440 TYR 0.014 0.001 TYR B 347 ARG 0.006 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 192) hydrogen bonds : angle 7.40997 ( 507) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.91586 ( 14) covalent geometry : bond 0.00337 ( 6952) covalent geometry : angle 0.61989 ( 9409) *********************** 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 233 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.764 Fit side-chains REVERT: B 146 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 384 GLU cc_start: 0.7353 (pp20) cc_final: 0.7041 (pp20) REVERT: E 216 ASP cc_start: 0.7244 (m-30) cc_final: 0.7019 (m-30) REVERT: E 457 PHE cc_start: 0.7842 (p90) cc_final: 0.7510 (p90) outliers start: 61 outliers final: 40 residues processed: 219 average time/residue: 1.0208 time to fit residues: 238.3301 Evaluate side-chains 207 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 284 LEU 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 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 458 ASP Chi-restraints excluded: chain E residue 144 TRP 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 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 348 SER Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 418 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 132 GLN B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115813 restraints weight = 9966.463| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.63 r_work: 0.3426 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6959 Z= 0.193 Angle : 0.645 8.578 9423 Z= 0.342 Chirality : 0.047 0.168 1033 Planarity : 0.005 0.049 1237 Dihedral : 9.101 59.367 993 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.88 % Favored : 90.00 % Rotamer: Outliers : 10.41 % Allowed : 32.97 % Favored : 56.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.28), residues: 860 helix: -1.02 (0.53), residues: 89 sheet: -0.38 (0.33), residues: 278 loop : -2.26 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 144 HIS 0.005 0.001 HIS B 218 PHE 0.028 0.002 PHE B 440 TYR 0.011 0.001 TYR E 449 ARG 0.006 0.001 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 192) hydrogen bonds : angle 6.91485 ( 507) SS BOND : bond 0.00407 ( 7) SS BOND : angle 1.73964 ( 14) covalent geometry : bond 0.00460 ( 6952) covalent geometry : angle 0.64181 ( 9409) *********************** 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 253 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 0.788 Fit side-chains REVERT: B 384 GLU cc_start: 0.7391 (pp20) cc_final: 0.7124 (pp20) REVERT: E 145 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7614 (tmt-80) REVERT: E 216 ASP cc_start: 0.7344 (m-30) cc_final: 0.7137 (m-30) outliers start: 77 outliers final: 50 residues processed: 227 average time/residue: 0.9204 time to fit residues: 222.2999 Evaluate side-chains 222 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 THR 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 260 GLU 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 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 340 VAL 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 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 309 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.123350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114262 restraints weight = 10047.727| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.62 r_work: 0.3404 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6959 Z= 0.280 Angle : 0.712 8.518 9423 Z= 0.377 Chirality : 0.050 0.180 1033 Planarity : 0.005 0.049 1237 Dihedral : 8.846 59.979 984 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.58 % Favored : 89.30 % Rotamer: Outliers : 11.76 % Allowed : 31.62 % Favored : 56.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 860 helix: -1.29 (0.51), residues: 90 sheet: -0.52 (0.33), residues: 269 loop : -2.34 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 144 HIS 0.006 0.002 HIS B 218 PHE 0.027 0.002 PHE B 440 TYR 0.015 0.002 TYR E 449 ARG 0.008 0.001 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 192) hydrogen bonds : angle 6.89822 ( 507) SS BOND : bond 0.00486 ( 7) SS BOND : angle 2.15087 ( 14) covalent geometry : bond 0.00674 ( 6952) covalent geometry : angle 0.70799 ( 9409) *********************** 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 257 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 0.770 Fit side-chains REVERT: B 144 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8132 (ttt) REVERT: B 287 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8167 (ptm-80) REVERT: B 384 GLU cc_start: 0.7413 (pp20) cc_final: 0.7120 (pp20) REVERT: E 36 ASP cc_start: 0.8196 (t0) cc_final: 0.7947 (t0) REVERT: E 216 ASP cc_start: 0.7437 (m-30) cc_final: 0.7193 (m-30) REVERT: E 305 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: E 445 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5528 (m-30) outliers start: 87 outliers final: 56 residues processed: 232 average time/residue: 0.8924 time to fit residues: 220.7165 Evaluate side-chains 220 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 THR 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 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 191 MET 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 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 287 ARG Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 317 SER 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 385 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 458 ASP 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 305 TYR Chi-restraints excluded: chain E residue 309 SER 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 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 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 510 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.0030 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115336 restraints weight = 9874.211| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.59 r_work: 0.3420 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6959 Z= 0.206 Angle : 0.667 9.823 9423 Z= 0.352 Chirality : 0.048 0.174 1033 Planarity : 0.005 0.052 1237 Dihedral : 8.518 58.902 982 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.23 % Favored : 89.65 % Rotamer: Outliers : 9.73 % Allowed : 33.38 % Favored : 56.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.28), residues: 860 helix: -1.03 (0.52), residues: 90 sheet: -0.52 (0.32), residues: 284 loop : -2.34 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 209 HIS 0.006 0.001 HIS B 218 PHE 0.022 0.002 PHE B 440 TYR 0.012 0.002 TYR E 234 ARG 0.007 0.001 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 192) hydrogen bonds : angle 6.71884 ( 507) SS BOND : bond 0.00460 ( 7) SS BOND : angle 1.82177 ( 14) covalent geometry : bond 0.00495 ( 6952) covalent geometry : angle 0.66333 ( 9409) *********************** 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 242 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 0.731 Fit side-chains REVERT: B 144 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8078 (ttt) REVERT: B 287 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8174 (ptm-80) REVERT: B 384 GLU cc_start: 0.7434 (pp20) cc_final: 0.7108 (pp20) REVERT: E 145 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7716 (tmt-80) REVERT: E 216 ASP cc_start: 0.7393 (m-30) cc_final: 0.7154 (m-30) REVERT: E 305 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: E 365 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7807 (mt-10) outliers start: 72 outliers final: 49 residues processed: 217 average time/residue: 1.0265 time to fit residues: 235.7198 Evaluate side-chains 213 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 401 LEU Chi-restraints excluded: chain B residue 409 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** E 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114914 restraints weight = 9905.087| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.60 r_work: 0.3416 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6959 Z= 0.224 Angle : 0.674 8.463 9423 Z= 0.357 Chirality : 0.048 0.179 1033 Planarity : 0.005 0.051 1237 Dihedral : 8.389 58.846 981 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.47 % Favored : 89.42 % Rotamer: Outliers : 10.54 % Allowed : 32.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.28), residues: 860 helix: -0.78 (0.52), residues: 84 sheet: -0.53 (0.32), residues: 284 loop : -2.34 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 144 HIS 0.006 0.001 HIS B 218 PHE 0.023 0.002 PHE B 440 TYR 0.017 0.002 TYR B 136 ARG 0.006 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 192) hydrogen bonds : angle 6.66637 ( 507) SS BOND : bond 0.00501 ( 7) SS BOND : angle 1.79257 ( 14) covalent geometry : bond 0.00538 ( 6952) covalent geometry : angle 0.67097 ( 9409) *********************** 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 240 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 162 time to evaluate : 0.800 Fit side-chains REVERT: B 131 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7266 (tpp80) REVERT: B 144 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8068 (ttt) REVERT: B 287 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8174 (ptm-80) REVERT: B 384 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7091 (pp20) REVERT: E 145 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (tmt-80) REVERT: E 216 ASP cc_start: 0.7377 (m-30) cc_final: 0.7119 (m-30) REVERT: E 305 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.6132 (m-80) outliers start: 78 outliers final: 57 residues processed: 215 average time/residue: 1.0118 time to fit residues: 230.6920 Evaluate side-chains 216 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 191 MET 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 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 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 SER 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 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 458 ASP Chi-restraints excluded: chain E residue 145 ARG 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 348 SER 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 438 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 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 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115815 restraints weight = 9838.322| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.59 r_work: 0.3428 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6959 Z= 0.182 Angle : 0.649 10.877 9423 Z= 0.342 Chirality : 0.047 0.170 1033 Planarity : 0.005 0.052 1237 Dihedral : 8.194 59.684 980 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.65 % Favored : 90.23 % Rotamer: Outliers : 8.92 % Allowed : 34.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 860 helix: -0.63 (0.54), residues: 84 sheet: -0.43 (0.32), residues: 280 loop : -2.28 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 209 HIS 0.005 0.001 HIS B 218 PHE 0.020 0.002 PHE B 440 TYR 0.018 0.002 TYR B 136 ARG 0.006 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 192) hydrogen bonds : angle 6.56770 ( 507) SS BOND : bond 0.00463 ( 7) SS BOND : angle 1.63536 ( 14) covalent geometry : bond 0.00437 ( 6952) covalent geometry : angle 0.64680 ( 9409) *********************** 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 232 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 0.763 Fit side-chains REVERT: B 131 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7433 (tpp80) REVERT: B 144 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8054 (ttt) REVERT: B 206 MET cc_start: 0.7590 (tmt) cc_final: 0.7337 (tmm) REVERT: B 287 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8187 (ptm-80) REVERT: B 384 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: E 145 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (tmt-80) REVERT: E 216 ASP cc_start: 0.7303 (m-30) cc_final: 0.7078 (m-30) REVERT: E 305 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6122 (m-80) REVERT: E 331 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8297 (mtm) outliers start: 66 outliers final: 53 residues processed: 211 average time/residue: 0.9656 time to fit residues: 216.5136 Evaluate side-chains 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 317 SER 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 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 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 331 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 348 SER 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 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 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.3980 chunk 86 optimal weight: 0.1980 chunk 83 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 71 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 73 optimal weight: 0.0070 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117695 restraints weight = 10006.945| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.63 r_work: 0.3454 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1665 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= 0.122 Angle : 0.620 10.790 9423 Z= 0.325 Chirality : 0.045 0.162 1033 Planarity : 0.005 0.053 1237 Dihedral : 7.698 59.459 977 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.95 % Favored : 90.93 % Rotamer: Outliers : 7.84 % Allowed : 35.54 % Favored : 56.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.28), residues: 860 helix: -0.37 (0.55), residues: 85 sheet: -0.40 (0.33), residues: 272 loop : -2.09 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.003 0.001 HIS B 218 PHE 0.018 0.001 PHE B 440 TYR 0.016 0.001 TYR B 136 ARG 0.005 0.000 ARG E 428 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 192) hydrogen bonds : angle 6.35321 ( 507) SS BOND : bond 0.00387 ( 7) SS BOND : angle 1.44909 ( 14) covalent geometry : bond 0.00291 ( 6952) covalent geometry : angle 0.61824 ( 9409) *********************** 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 226 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.824 Fit side-chains REVERT: B 131 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7278 (tpp80) REVERT: B 144 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8014 (ttt) REVERT: B 206 MET cc_start: 0.7609 (tmt) cc_final: 0.7359 (tmm) REVERT: B 287 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8169 (ptm-80) REVERT: B 384 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7097 (pp20) REVERT: E 216 ASP cc_start: 0.7218 (m-30) cc_final: 0.7007 (m-30) REVERT: E 305 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: E 331 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8272 (mtm) outliers start: 58 outliers final: 39 residues processed: 206 average time/residue: 1.0132 time to fit residues: 221.3799 Evaluate side-chains 211 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 340 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 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 348 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN B 298 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115802 restraints weight = 9979.147| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.62 r_work: 0.3426 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6959 Z= 0.194 Angle : 0.676 10.383 9423 Z= 0.351 Chirality : 0.048 0.174 1033 Planarity : 0.005 0.048 1237 Dihedral : 7.680 58.582 971 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.12 % Favored : 89.77 % Rotamer: Outliers : 7.16 % Allowed : 36.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.28), residues: 860 helix: -0.53 (0.53), residues: 85 sheet: -0.41 (0.33), residues: 271 loop : -2.12 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 144 HIS 0.005 0.001 HIS B 218 PHE 0.021 0.002 PHE B 440 TYR 0.016 0.002 TYR B 136 ARG 0.008 0.001 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 192) hydrogen bonds : angle 6.41734 ( 507) SS BOND : bond 0.00441 ( 7) SS BOND : angle 1.75762 ( 14) covalent geometry : bond 0.00467 ( 6952) covalent geometry : angle 0.67349 ( 9409) *********************** 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 214 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.744 Fit side-chains REVERT: B 144 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8042 (ttt) REVERT: B 206 MET cc_start: 0.7612 (tmt) cc_final: 0.7362 (tmm) REVERT: B 287 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8183 (ptm-80) REVERT: B 384 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7151 (pp20) REVERT: E 216 ASP cc_start: 0.7237 (m-30) cc_final: 0.7016 (m-30) REVERT: E 305 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6136 (m-80) outliers start: 53 outliers final: 44 residues processed: 200 average time/residue: 1.0131 time to fit residues: 215.0181 Evaluate side-chains 205 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 317 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 377 ILE 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 458 ASP 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 305 TYR Chi-restraints excluded: chain E residue 348 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 0.0050 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116539 restraints weight = 10141.607| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.64 r_work: 0.3436 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6959 Z= 0.150 Angle : 0.650 10.022 9423 Z= 0.338 Chirality : 0.047 0.202 1033 Planarity : 0.005 0.052 1237 Dihedral : 7.348 58.590 969 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 6.22 % Allowed : 37.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.28), residues: 860 helix: -0.40 (0.54), residues: 85 sheet: -0.40 (0.32), residues: 282 loop : -2.12 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.005 0.001 HIS B 218 PHE 0.018 0.002 PHE B 440 TYR 0.015 0.001 TYR B 136 ARG 0.007 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 192) hydrogen bonds : angle 6.44086 ( 507) SS BOND : bond 0.00412 ( 7) SS BOND : angle 1.62170 ( 14) covalent geometry : bond 0.00368 ( 6952) covalent geometry : angle 0.64748 ( 9409) ********************** 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 211 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.795 Fit side-chains REVERT: B 144 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8037 (ttt) REVERT: B 206 MET cc_start: 0.7628 (tmt) cc_final: 0.7373 (tmm) REVERT: B 287 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8185 (ptm-80) REVERT: B 384 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: E 148 MET cc_start: 0.7917 (ttm) cc_final: 0.7611 (ttp) REVERT: E 216 ASP cc_start: 0.7213 (m-30) cc_final: 0.7004 (m-30) REVERT: E 305 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6145 (m-80) outliers start: 46 outliers final: 43 residues processed: 200 average time/residue: 1.0440 time to fit residues: 221.0345 Evaluate side-chains 209 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 317 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 348 SER 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 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 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 348 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 0.2980 chunk 57 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 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 = 0.3638 r_free = 0.3638 target = 0.125534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116362 restraints weight = 10067.932| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.63 r_work: 0.3435 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6959 Z= 0.170 Angle : 0.662 9.803 9423 Z= 0.346 Chirality : 0.047 0.174 1033 Planarity : 0.005 0.051 1237 Dihedral : 7.271 58.714 969 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 6.35 % Allowed : 37.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.28), residues: 860 helix: -0.45 (0.54), residues: 85 sheet: -0.47 (0.32), residues: 284 loop : -2.12 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.005 0.001 HIS B 218 PHE 0.019 0.002 PHE B 440 TYR 0.015 0.001 TYR B 136 ARG 0.009 0.000 ARG B 378 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 192) hydrogen bonds : angle 6.48151 ( 507) SS BOND : bond 0.00425 ( 7) SS BOND : angle 1.67424 ( 14) covalent geometry : bond 0.00417 ( 6952) covalent geometry : angle 0.65938 ( 9409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5549.20 seconds wall clock time: 96 minutes 15.86 seconds (5775.86 seconds total)