Starting phenix.real_space_refine on Fri Dec 27 22:31:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ij5_35465/12_2024/8ij5_35465.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ij5_35465/12_2024/8ij5_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_35465/12_2024/8ij5_35465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ij5_35465/12_2024/8ij5_35465.map" model { file = "/net/cci-nas-00/data/ceres_data/8ij5_35465/12_2024/8ij5_35465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ij5_35465/12_2024/8ij5_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.72, per 1000 atoms: 0.69 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: 1.58 Conformation dependent library (CDL) restraints added in 929.8 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: 0.85 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: 2.09 Time building geometry restraints manager: 1.86 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: 1.580 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.480 Find NCS groups from input model: 0.070 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- 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 6952 Z= 0.199 Angle : 0.615 10.395 9409 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 *********************** 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 : 0.726 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: 1.0517 time to fit residues: 270.9862 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 : 0.876 ------------------------------------------------------------------------------- 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: 1.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 6952 Z= 0.213 Angle : 0.620 8.359 9409 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 *********************** 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 : 0.822 Fit side-chains REVERT: B 146 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7017 (mt) REVERT: B 384 GLU cc_start: 0.7319 (pp20) cc_final: 0.7014 (pp20) REVERT: E 216 ASP cc_start: 0.7258 (m-30) cc_final: 0.7023 (m-30) REVERT: E 457 PHE cc_start: 0.7911 (p90) cc_final: 0.7556 (p90) outliers start: 61 outliers final: 40 residues processed: 219 average time/residue: 1.0013 time to fit residues: 233.2177 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 : 0.722 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 6952 Z= 0.484 Angle : 0.732 7.748 9409 Z= 0.390 Chirality : 0.051 0.183 1033 Planarity : 0.006 0.050 1237 Dihedral : 9.622 59.630 993 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.05 % Favored : 88.84 % Rotamer: Outliers : 11.08 % Allowed : 33.51 % Favored : 55.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.28), residues: 860 helix: -1.37 (0.51), residues: 90 sheet: -0.48 (0.32), residues: 281 loop : -2.43 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 144 HIS 0.005 0.002 HIS B 218 PHE 0.033 0.003 PHE B 440 TYR 0.016 0.002 TYR E 449 ARG 0.007 0.001 ARG B 242 *********************** 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: 82 poor density : 171 time to evaluate : 0.728 Fit side-chains REVERT: B 384 GLU cc_start: 0.7374 (pp20) cc_final: 0.7077 (pp20) REVERT: E 147 GLU cc_start: 0.6941 (pm20) cc_final: 0.6563 (pm20) REVERT: E 305 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6202 (m-80) REVERT: E 445 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5640 (m-30) outliers start: 82 outliers final: 55 residues processed: 226 average time/residue: 0.9233 time to fit residues: 222.7022 Evaluate side-chains 226 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 299 CYS Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 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 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 176 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 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 413 LEU 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 78 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 298 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6952 Z= 0.329 Angle : 0.667 9.400 9409 Z= 0.353 Chirality : 0.047 0.173 1033 Planarity : 0.005 0.052 1237 Dihedral : 9.043 59.103 988 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.12 % Favored : 89.77 % Rotamer: Outliers : 11.62 % Allowed : 31.89 % 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: -2.37 (0.28), residues: 860 helix: -1.24 (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 0.009 0.002 TRP E 209 HIS 0.006 0.001 HIS B 218 PHE 0.026 0.002 PHE B 440 TYR 0.012 0.002 TYR E 449 ARG 0.006 0.001 ARG B 378 *********************** 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 259 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 0.778 Fit side-chains REVERT: B 144 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: B 384 GLU cc_start: 0.7404 (pp20) cc_final: 0.7110 (pp20) REVERT: E 145 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7810 (tmt-80) REVERT: E 147 GLU cc_start: 0.6679 (pm20) cc_final: 0.6312 (pm20) REVERT: E 216 ASP cc_start: 0.7277 (m-30) cc_final: 0.7075 (m-30) REVERT: E 305 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: E 365 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7763 (mt-10) REVERT: E 413 LEU cc_start: 0.7647 (pt) cc_final: 0.7440 (pt) outliers start: 86 outliers final: 56 residues processed: 230 average time/residue: 0.9722 time to fit residues: 237.4796 Evaluate side-chains 231 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 151 LYS 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 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 303 SER 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 341 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 367 LEU 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 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 258 VAL 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 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain E residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.0030 chunk 58 optimal weight: 0.0770 chunk 0 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 158 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6952 Z= 0.260 Angle : 0.636 8.242 9409 Z= 0.337 Chirality : 0.046 0.172 1033 Planarity : 0.005 0.052 1237 Dihedral : 8.492 58.953 984 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.65 % Favored : 90.23 % Rotamer: Outliers : 10.41 % Allowed : 32.84 % Favored : 56.76 % 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: -0.80 (0.53), residues: 84 sheet: -0.43 (0.33), residues: 279 loop : -2.26 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 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 0.006 0.000 ARG B 131 *********************** 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 255 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 178 time to evaluate : 0.743 Fit side-chains REVERT: B 131 ARG cc_start: 0.7534 (tpp80) cc_final: 0.7281 (tpp80) REVERT: B 144 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8073 (ttt) REVERT: B 287 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8230 (ptm-80) REVERT: B 384 GLU cc_start: 0.7426 (pp20) cc_final: 0.7113 (pp20) REVERT: E 145 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7787 (tmt-80) REVERT: E 216 ASP cc_start: 0.7301 (m-30) cc_final: 0.7065 (m-30) REVERT: E 305 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: E 331 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: E 365 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7787 (mt-10) outliers start: 77 outliers final: 50 residues processed: 230 average time/residue: 1.0157 time to fit residues: 247.8438 Evaluate side-chains 220 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 152 ASP Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain B residue 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 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 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 323 VAL Chi-restraints excluded: chain E residue 331 MET 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 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 409 ARG Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 425 TRP Chi-restraints excluded: chain E residue 445 ASP Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 502 CYS Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 565 CYS Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6952 Z= 0.331 Angle : 0.669 9.735 9409 Z= 0.353 Chirality : 0.048 0.180 1033 Planarity : 0.005 0.051 1237 Dihedral : 8.325 58.913 981 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.23 % Favored : 89.65 % Rotamer: Outliers : 9.73 % Allowed : 33.65 % 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: -2.27 (0.28), residues: 860 helix: -0.98 (0.51), residues: 90 sheet: -0.44 (0.33), residues: 279 loop : -2.37 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 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 0.001 ARG B 378 *********************** 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 239 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 167 time to evaluate : 0.688 Fit side-chains REVERT: B 131 ARG cc_start: 0.7519 (tpp80) cc_final: 0.7318 (tpp80) REVERT: B 144 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8074 (ttt) REVERT: B 206 MET cc_start: 0.7410 (tmt) cc_final: 0.7162 (tmm) REVERT: B 287 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8224 (ptm-80) REVERT: B 384 GLU cc_start: 0.7437 (pp20) cc_final: 0.7120 (pp20) REVERT: E 145 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7803 (tmt-80) REVERT: E 216 ASP cc_start: 0.7346 (m-30) cc_final: 0.7131 (m-30) REVERT: E 305 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: E 331 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8278 (mtm) outliers start: 72 outliers final: 55 residues processed: 219 average time/residue: 1.0214 time to fit residues: 237.2021 Evaluate side-chains 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 163 LYS 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 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 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 331 MET Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 ASP Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain E residue 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 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 83 optimal weight: 0.2980 chunk 52 optimal weight: 0.4980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 GLN B 158 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6952 Z= 0.257 Angle : 0.639 10.462 9409 Z= 0.337 Chirality : 0.047 0.171 1033 Planarity : 0.005 0.052 1237 Dihedral : 8.098 58.832 980 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.53 % Favored : 90.35 % Rotamer: Outliers : 8.92 % Allowed : 34.73 % Favored : 56.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.28), residues: 860 helix: -0.59 (0.54), residues: 84 sheet: -0.37 (0.33), residues: 278 loop : -2.25 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.006 0.001 HIS B 218 PHE 0.021 0.002 PHE B 440 TYR 0.018 0.001 TYR B 136 ARG 0.005 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 0.803 Fit side-chains REVERT: B 144 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: B 206 MET cc_start: 0.7404 (tmt) cc_final: 0.7160 (tmm) REVERT: B 287 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8216 (ptm-80) REVERT: B 384 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: E 64 MET cc_start: 0.8071 (mtm) cc_final: 0.7564 (mpp) REVERT: E 216 ASP cc_start: 0.7305 (m-30) cc_final: 0.7086 (m-30) REVERT: E 305 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: E 331 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8275 (mtm) outliers start: 66 outliers final: 53 residues processed: 206 average time/residue: 1.0057 time to fit residues: 220.0142 Evaluate side-chains 218 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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 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 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 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 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 258 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6952 Z= 0.375 Angle : 0.687 9.373 9409 Z= 0.362 Chirality : 0.049 0.180 1033 Planarity : 0.005 0.050 1237 Dihedral : 8.155 58.893 977 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.58 % Favored : 89.30 % Rotamer: Outliers : 9.32 % Allowed : 34.59 % Favored : 56.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.52), residues: 91 sheet: -0.48 (0.33), residues: 269 loop : -2.29 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 144 HIS 0.005 0.001 HIS B 218 PHE 0.024 0.002 PHE B 440 TYR 0.017 0.002 TYR B 136 ARG 0.009 0.001 ARG B 131 *********************** 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 234 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 0.792 Fit side-chains REVERT: B 131 ARG cc_start: 0.7403 (tpp80) cc_final: 0.7123 (tpp80) REVERT: B 144 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8024 (ttt) REVERT: B 206 MET cc_start: 0.7430 (tmt) cc_final: 0.7184 (tmm) REVERT: B 287 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8243 (ptm-80) REVERT: B 384 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: E 216 ASP cc_start: 0.7405 (m-30) cc_final: 0.7161 (m-30) REVERT: E 305 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: E 331 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8289 (mtm) outliers start: 69 outliers final: 55 residues processed: 211 average time/residue: 1.0580 time to fit residues: 236.9898 Evaluate side-chains 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 159 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 LYS 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 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 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 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 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 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 34 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 6952 Z= 0.408 Angle : 0.723 10.967 9409 Z= 0.378 Chirality : 0.050 0.185 1033 Planarity : 0.005 0.050 1237 Dihedral : 8.113 58.976 975 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.16 % Favored : 88.72 % Rotamer: Outliers : 8.38 % Allowed : 35.81 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.28), residues: 860 helix: -1.16 (0.51), residues: 91 sheet: -0.46 (0.32), residues: 280 loop : -2.36 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 144 HIS 0.005 0.001 HIS B 218 PHE 0.025 0.002 PHE B 440 TYR 0.021 0.002 TYR B 136 ARG 0.010 0.001 ARG B 378 *********************** 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 219 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 0.761 Fit side-chains REVERT: B 131 ARG cc_start: 0.7419 (tpp80) cc_final: 0.7159 (tpp80) REVERT: B 144 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7985 (ttt) REVERT: B 206 MET cc_start: 0.7404 (tmt) cc_final: 0.7172 (tmm) REVERT: B 287 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8249 (ptm-80) REVERT: B 384 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: E 216 ASP cc_start: 0.7438 (m-30) cc_final: 0.7205 (m-30) REVERT: E 305 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: E 331 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8290 (mtm) outliers start: 62 outliers final: 56 residues processed: 202 average time/residue: 1.0972 time to fit residues: 234.8326 Evaluate side-chains 215 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 154 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 163 LYS 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 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 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 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 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 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 86 optimal weight: 0.0030 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6952 Z= 0.262 Angle : 0.668 11.718 9409 Z= 0.346 Chirality : 0.047 0.169 1033 Planarity : 0.005 0.053 1237 Dihedral : 7.868 59.101 975 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 8.38 % Allowed : 35.81 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.53), residues: 85 sheet: -0.40 (0.32), residues: 279 loop : -2.27 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 264 HIS 0.005 0.001 HIS B 218 PHE 0.020 0.002 PHE B 440 TYR 0.023 0.002 TYR B 136 ARG 0.008 0.001 ARG B 378 ********************** 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 223 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.796 Fit side-chains REVERT: B 131 ARG cc_start: 0.7387 (tpp80) cc_final: 0.7120 (tpp80) REVERT: B 144 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8014 (ttt) REVERT: B 206 MET cc_start: 0.7383 (tmt) cc_final: 0.7168 (tmm) REVERT: B 287 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8235 (ptm-80) REVERT: B 384 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7113 (pp20) REVERT: E 64 MET cc_start: 0.8088 (mtm) cc_final: 0.7580 (mpp) REVERT: E 148 MET cc_start: 0.7495 (ttm) cc_final: 0.7250 (ttp) REVERT: E 216 ASP cc_start: 0.7387 (m-30) cc_final: 0.7147 (m-30) REVERT: E 305 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: E 331 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8273 (mtm) outliers start: 62 outliers final: 49 residues processed: 203 average time/residue: 1.0294 time to fit residues: 222.1285 Evaluate side-chains 210 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 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 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 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 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 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 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114648 restraints weight = 9854.848| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.58 r_work: 0.3410 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 6952 Z= 0.372 Angle : 0.711 11.190 9409 Z= 0.370 Chirality : 0.049 0.182 1033 Planarity : 0.005 0.056 1237 Dihedral : 7.931 58.781 975 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 7.84 % Allowed : 36.35 % Favored : 55.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.26 (0.28), residues: 860 helix: -0.81 (0.53), residues: 85 sheet: -0.45 (0.32), residues: 280 loop : -2.36 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 209 HIS 0.005 0.001 HIS B 218 PHE 0.023 0.002 PHE B 440 TYR 0.023 0.002 TYR B 136 ARG 0.011 0.001 ARG B 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.49 seconds wall clock time: 68 minutes 59.17 seconds (4139.17 seconds total)