Starting phenix.real_space_refine on Tue Aug 26 20:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.map" model { file = "/net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mr8_48555/08_2025/9mr8_48555.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 12600 2.51 5 N 3750 2.21 5 O 3870 1.98 5 H 21300 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41580 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1386 Classifications: {'peptide': 90} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Restraints were copied for chains: A, B, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1, 2, 3 Time building chain proxies: 2.48, per 1000 atoms: 0.06 Number of scatterers: 41580 At special positions: 0 Unit cell: (106, 99.64, 161.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 O 3870 8.00 N 3750 7.00 C 12600 6.00 H 21300 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.01 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 21240 1.11 - 1.28: 3480 1.28 - 1.46: 4620 1.46 - 1.63: 12420 1.63 - 1.81: 60 Bond restraints: 41820 Sorted by residual: bond pdb=" NE2 GLN 3 276 " pdb="HE21 GLN 3 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" ND2 ASN E 296 " pdb="HD21 ASN E 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" ND2 ASN L 296 " pdb="HD21 ASN L 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N GLN G 288 " pdb=" H GLN G 288 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN T 296 " pdb="HD21 ASN T 296 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 41815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 61109 2.47 - 4.95: 11675 4.95 - 7.42: 3198 7.42 - 9.89: 338 9.89 - 12.37: 60 Bond angle restraints: 76380 Sorted by residual: angle pdb=" CA ASP 3 283 " pdb=" CB ASP 3 283 " pdb=" CG ASP 3 283 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASP F 283 " pdb=" CB ASP F 283 " pdb=" CG ASP F 283 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP G 283 " pdb=" CB ASP G 283 " pdb=" CG ASP G 283 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 angle pdb=" CA ASP D 283 " pdb=" CB ASP D 283 " pdb=" CG ASP D 283 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA ASP N 283 " pdb=" CB ASP N 283 " pdb=" CG ASP N 283 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.00e+00 1.00e+00 3.04e+01 ... (remaining 76375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 16702 16.29 - 32.58: 1298 32.58 - 48.86: 450 48.86 - 65.15: 570 65.15 - 81.44: 120 Dihedral angle restraints: 19140 sinusoidal: 11070 harmonic: 8070 Sorted by residual: dihedral pdb=" CA LYS 3 274 " pdb=" C LYS 3 274 " pdb=" N VAL 3 275 " pdb=" CA VAL 3 275 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LYS G 274 " pdb=" C LYS G 274 " pdb=" N VAL G 275 " pdb=" CA VAL G 275 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LYS T 274 " pdb=" C LYS T 274 " pdb=" N VAL T 275 " pdb=" CA VAL T 275 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 19137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1306 0.058 - 0.116: 824 0.116 - 0.173: 570 0.173 - 0.231: 270 0.231 - 0.289: 150 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA PRO X 312 " pdb=" N PRO X 312 " pdb=" C PRO X 312 " pdb=" CB PRO X 312 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA PRO 2 312 " pdb=" N PRO 2 312 " pdb=" C PRO 2 312 " pdb=" CB PRO 2 312 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE Y 278 " pdb=" CA ILE Y 278 " pdb=" CG1 ILE Y 278 " pdb=" CG2 ILE Y 278 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3117 not shown) Planarity restraints: 6090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 274 " 0.027 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" N VAL A 275 " -0.082 2.00e-02 2.50e+03 pdb=" CA VAL A 275 " 0.024 2.00e-02 2.50e+03 pdb=" H VAL A 275 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 274 " 0.027 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" N VAL I 275 " -0.082 2.00e-02 2.50e+03 pdb=" CA VAL I 275 " 0.024 2.00e-02 2.50e+03 pdb=" H VAL I 275 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS W 274 " 0.027 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" N VAL W 275 " -0.082 2.00e-02 2.50e+03 pdb=" CA VAL W 275 " 0.024 2.00e-02 2.50e+03 pdb=" H VAL W 275 " 0.031 2.00e-02 2.50e+03 ... (remaining 6087 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.74: 495 1.74 - 2.45: 21449 2.45 - 3.17: 137017 3.17 - 3.88: 176991 3.88 - 4.60: 269218 Nonbonded interactions: 605170 Sorted by model distance: nonbonded pdb=" HB3 LEU C 284 " pdb="HD12 LEU Q 284 " model vdw 1.024 2.440 nonbonded pdb=" HB3 LEU Y 284 " pdb="HD12 LEU Z 284 " model vdw 1.024 2.440 nonbonded pdb=" HB3 LEU E 284 " pdb="HD12 LEU F 284 " model vdw 1.024 2.440 nonbonded pdb=" HB3 LEU U 284 " pdb="HD12 LEU V 284 " model vdw 1.024 2.440 nonbonded pdb=" HB3 LEU H 284 " pdb="HD12 LEU I 284 " model vdw 1.024 2.440 ... (remaining 605165 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' } 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: 4.410 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: 0.140 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 20.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4497 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 : 0.012 0.033 20520 Z= 0.787 Angle : 2.212 7.156 27420 Z= 1.453 Chirality : 0.113 0.289 3120 Planarity : 0.009 0.035 3510 Dihedral : 15.800 81.439 7950 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 36.37 Ramachandran Plot: Outliers : 2.27 % Allowed : 5.68 % Favored : 92.05 % Rotamer: Outliers : 6.33 % Allowed : 3.80 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.09), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG Y 349 TYR 0.047 0.021 TYR U 310 PHE 0.016 0.007 PHE D 346 HIS 0.009 0.003 HIS 1 362 Details of bonding type rmsd covalent geometry : bond 0.01195 (20520) covalent geometry : angle 2.21209 (27420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 340 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.0882 (OUTLIER) cc_final: 0.0626 (mmtm) REVERT: G 278 ILE cc_start: 0.2963 (OUTLIER) cc_final: 0.2571 (pt) REVERT: J 294 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.5102 (mptp) REVERT: K 280 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.5211 (tttm) REVERT: L 279 ASN cc_start: 0.5770 (OUTLIER) cc_final: 0.5535 (t0) REVERT: N 274 LYS cc_start: 0.6359 (tttt) cc_final: 0.6131 (mmtp) REVERT: O 279 ASN cc_start: 0.6915 (OUTLIER) cc_final: 0.6684 (t0) REVERT: P 279 ASN cc_start: 0.7260 (OUTLIER) cc_final: 0.7006 (m-40) REVERT: P 319 THR cc_start: 0.8333 (p) cc_final: 0.8000 (m) REVERT: S 279 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6752 (m-40) REVERT: U 279 ASN cc_start: 0.6408 (OUTLIER) cc_final: 0.6015 (t0) REVERT: W 279 ASN cc_start: 0.6002 (OUTLIER) cc_final: 0.5777 (m110) REVERT: Z 294 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6307 (tptp) outliers start: 150 outliers final: 52 residues processed: 448 average time/residue: 1.0685 time to fit residues: 550.1419 Evaluate side-chains 280 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 351 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 294 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 294 LYS Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 294 LYS Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 278 ILE Chi-restraints excluded: chain I residue 280 LYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 278 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain O residue 278 ILE Chi-restraints excluded: chain O residue 279 ASN Chi-restraints excluded: chain O residue 351 GLN Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 279 ASN Chi-restraints excluded: chain P residue 351 GLN Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain Q residue 351 GLN Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 351 GLN Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain S residue 279 ASN Chi-restraints excluded: chain S residue 351 GLN Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 280 LYS Chi-restraints excluded: chain T residue 351 GLN Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain U residue 279 ASN Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 351 GLN Chi-restraints excluded: chain V residue 278 ILE Chi-restraints excluded: chain V residue 280 LYS Chi-restraints excluded: chain V residue 351 GLN Chi-restraints excluded: chain W residue 278 ILE Chi-restraints excluded: chain W residue 279 ASN Chi-restraints excluded: chain X residue 280 LYS Chi-restraints excluded: chain Y residue 278 ILE Chi-restraints excluded: chain Z residue 294 LYS Chi-restraints excluded: chain 0 residue 278 ILE Chi-restraints excluded: chain 2 residue 278 ILE Chi-restraints excluded: chain 2 residue 280 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN A 307 GLN A 359 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 279 ASN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 351 GLN P 279 ASN ** P 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 351 GLN ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 351 GLN R 279 ASN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 351 GLN ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 351 GLN T 296 ASN ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 351 GLN ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 351 GLN V 279 ASN ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 351 GLN ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 362 HIS Y 279 ASN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 362 HIS 0 279 ASN ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 279 ASN 3 279 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5542 r_free = 0.5542 target = 0.221587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.200316 restraints weight = 74676.196| |-----------------------------------------------------------------------------| r_work (start): 0.5340 rms_B_bonded: 2.75 r_work: 0.5246 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.5246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20520 Z= 0.215 Angle : 0.918 8.293 27420 Z= 0.494 Chirality : 0.057 0.187 3120 Planarity : 0.006 0.053 3510 Dihedral : 10.608 55.010 2903 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.95 % Favored : 90.91 % Rotamer: Outliers : 5.11 % Allowed : 11.65 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.11), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.08), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG W 349 TYR 0.007 0.002 TYR Y 310 PHE 0.009 0.003 PHE V 346 HIS 0.009 0.002 HIS 1 330 Details of bonding type rmsd covalent geometry : bond 0.00444 (20520) covalent geometry : angle 0.91806 (27420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 269 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASN cc_start: 0.2560 (OUTLIER) cc_final: 0.1611 (p0) REVERT: B 294 LYS cc_start: 0.2936 (OUTLIER) cc_final: 0.2275 (mptt) REVERT: D 294 LYS cc_start: 0.3411 (OUTLIER) cc_final: 0.2744 (mmtp) REVERT: E 359 ASN cc_start: 0.2937 (OUTLIER) cc_final: 0.2063 (p0) REVERT: G 278 ILE cc_start: 0.2261 (OUTLIER) cc_final: 0.1753 (pt) REVERT: I 278 ILE cc_start: 0.4243 (OUTLIER) cc_final: 0.3528 (pt) REVERT: I 343 LYS cc_start: 0.5607 (tttt) cc_final: 0.5405 (ttpp) REVERT: I 359 ASN cc_start: 0.5334 (OUTLIER) cc_final: 0.5078 (p0) REVERT: J 294 LYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5813 (mptt) REVERT: J 349 ARG cc_start: 0.6216 (ttp-170) cc_final: 0.5963 (ttm170) REVERT: K 280 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5267 (tmtt) REVERT: K 349 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6593 (ttp-170) REVERT: L 279 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.6288 (m110) REVERT: M 353 LYS cc_start: 0.7096 (mptt) cc_final: 0.6330 (tmtt) REVERT: M 359 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.5593 (p0) REVERT: N 274 LYS cc_start: 0.6760 (tttt) cc_final: 0.5753 (mptm) REVERT: N 353 LYS cc_start: 0.7148 (mptt) cc_final: 0.6244 (ttpt) REVERT: N 359 ASN cc_start: 0.6286 (OUTLIER) cc_final: 0.5803 (p0) REVERT: O 359 ASN cc_start: 0.6415 (OUTLIER) cc_final: 0.5822 (p0) REVERT: P 284 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6494 (tt) REVERT: Q 359 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6532 (p0) REVERT: R 294 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7495 (mptt) REVERT: S 294 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7894 (mptt) REVERT: T 288 GLN cc_start: 0.7439 (mt0) cc_final: 0.7106 (mt0) REVERT: T 294 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (mmtp) REVERT: U 296 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6543 (p0) REVERT: V 282 LEU cc_start: 0.6752 (tt) cc_final: 0.6260 (mp) REVERT: W 279 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.6202 (t0) REVERT: Z 294 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6916 (tmtt) REVERT: 1 278 ILE cc_start: 0.5311 (pt) cc_final: 0.5091 (pt) REVERT: 2 281 LYS cc_start: 0.4223 (mttp) cc_final: 0.3985 (mtpt) outliers start: 121 outliers final: 43 residues processed: 361 average time/residue: 0.8427 time to fit residues: 361.3080 Evaluate side-chains 266 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 278 ILE Chi-restraints excluded: chain I residue 294 LYS Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 349 ARG Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 278 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain N residue 359 ASN Chi-restraints excluded: chain O residue 278 ILE Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 279 ASN Chi-restraints excluded: chain R residue 294 LYS Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain S residue 294 LYS Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 280 LYS Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 320 SER Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain U residue 296 ASN Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 361 THR Chi-restraints excluded: chain V residue 278 ILE Chi-restraints excluded: chain V residue 280 LYS Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain W residue 278 ILE Chi-restraints excluded: chain W residue 279 ASN Chi-restraints excluded: chain W residue 294 LYS Chi-restraints excluded: chain W residue 296 ASN Chi-restraints excluded: chain X residue 280 LYS Chi-restraints excluded: chain Z residue 294 LYS Chi-restraints excluded: chain 0 residue 284 LEU Chi-restraints excluded: chain 1 residue 284 LEU Chi-restraints excluded: chain 1 residue 330 HIS Chi-restraints excluded: chain 2 residue 284 LEU Chi-restraints excluded: chain 2 residue 330 HIS Chi-restraints excluded: chain 2 residue 359 ASN Chi-restraints excluded: chain 3 residue 330 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 75 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 279 ASN ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 329 HIS ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 ASN ** P 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 307 GLN ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 279 ASN Z 296 ASN 2 279 ASN 3 279 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5510 r_free = 0.5510 target = 0.208368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.186173 restraints weight = 76734.117| |-----------------------------------------------------------------------------| r_work (start): 0.5267 rms_B_bonded: 2.69 r_work: 0.5167 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.5167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20520 Z= 0.165 Angle : 0.822 11.522 27420 Z= 0.433 Chirality : 0.057 0.184 3120 Planarity : 0.006 0.052 3510 Dihedral : 8.915 53.010 2816 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 1.14 % Allowed : 11.25 % Favored : 87.61 % Rotamer: Outliers : 3.50 % Allowed : 15.70 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.54 (0.11), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.08), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 349 TYR 0.011 0.001 TYR A 310 PHE 0.014 0.003 PHE W 346 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00360 (20520) covalent geometry : angle 0.82201 (27420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 266 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.2181 (OUTLIER) cc_final: 0.1352 (mptt) REVERT: D 294 LYS cc_start: 0.3976 (OUTLIER) cc_final: 0.3484 (mppt) REVERT: I 359 ASN cc_start: 0.5602 (OUTLIER) cc_final: 0.5249 (p0) REVERT: K 349 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7047 (ttt180) REVERT: L 279 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6412 (m110) REVERT: L 284 LEU cc_start: 0.6355 (mp) cc_final: 0.6038 (tt) REVERT: L 352 SER cc_start: 0.8162 (t) cc_final: 0.7904 (m) REVERT: L 356 SER cc_start: 0.8667 (t) cc_final: 0.8256 (p) REVERT: M 340 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7354 (mtpp) REVERT: N 274 LYS cc_start: 0.7140 (tttt) cc_final: 0.6098 (mptm) REVERT: N 294 LYS cc_start: 0.7036 (tptm) cc_final: 0.6574 (tptt) REVERT: N 305 SER cc_start: 0.7390 (p) cc_final: 0.7103 (m) REVERT: O 288 GLN cc_start: 0.7716 (mt0) cc_final: 0.7450 (mt0) REVERT: O 294 LYS cc_start: 0.7207 (tptm) cc_final: 0.6674 (tptt) REVERT: O 359 ASN cc_start: 0.6489 (OUTLIER) cc_final: 0.5686 (p0) REVERT: P 284 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6758 (tm) REVERT: R 288 GLN cc_start: 0.8427 (pt0) cc_final: 0.7505 (pt0) REVERT: S 287 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8180 (t) REVERT: T 280 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6792 (tmtt) REVERT: U 294 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7566 (mptt) REVERT: V 280 LYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6532 (tmtt) REVERT: W 279 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6515 (t0) REVERT: W 280 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5802 (mtmm) REVERT: W 361 THR cc_start: 0.4170 (t) cc_final: 0.3623 (m) REVERT: Y 342 GLU cc_start: 0.6414 (tm-30) cc_final: 0.6133 (tm-30) REVERT: Z 294 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7437 (tmtt) REVERT: 0 294 LYS cc_start: 0.7984 (tmtt) cc_final: 0.7498 (ttpt) outliers start: 83 outliers final: 36 residues processed: 325 average time/residue: 0.9389 time to fit residues: 359.1521 Evaluate side-chains 266 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 279 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain J residue 294 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 349 ARG Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 284 LEU Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain Q residue 352 SER Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 361 THR Chi-restraints excluded: chain T residue 280 LYS Chi-restraints excluded: chain T residue 305 SER Chi-restraints excluded: chain T residue 320 SER Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 294 LYS Chi-restraints excluded: chain V residue 278 ILE Chi-restraints excluded: chain V residue 280 LYS Chi-restraints excluded: chain V residue 294 LYS Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain W residue 279 ASN Chi-restraints excluded: chain W residue 280 LYS Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain W residue 294 LYS Chi-restraints excluded: chain W residue 330 HIS Chi-restraints excluded: chain Z residue 294 LYS Chi-restraints excluded: chain 0 residue 330 HIS Chi-restraints excluded: chain 1 residue 330 HIS Chi-restraints excluded: chain 2 residue 330 HIS Chi-restraints excluded: chain 2 residue 359 ASN Chi-restraints excluded: chain 3 residue 330 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 260 optimal weight: 0.6980 chunk 249 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 299 HIS ** H 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 GLN H 351 GLN I 276 GLN ** I 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 327 ASN ** M 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 327 ASN ** O 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 307 GLN O 359 ASN P 279 ASN ** P 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 GLN Q 307 GLN Q 359 ASN R 296 ASN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 276 GLN ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 288 GLN ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 307 GLN ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 307 GLN ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 279 ASN ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 327 ASN Z 279 ASN Z 296 ASN ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 327 ASN ** 0 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 327 ASN 1 279 ASN 1 327 ASN 1 329 HIS ** 2 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 327 ASN 2 329 HIS ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 279 ASN 3 327 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5655 r_free = 0.5655 target = 0.337964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5875 r_free = 0.5875 target = 0.301897 restraints weight = 68916.695| |-----------------------------------------------------------------------------| r_work (start): 0.5255 rms_B_bonded: 0.84 r_work: 0.5152 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.5072 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.5072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.9726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 20520 Z= 0.272 Angle : 1.039 10.085 27420 Z= 0.558 Chirality : 0.061 0.232 3120 Planarity : 0.008 0.078 3510 Dihedral : 10.005 54.385 2780 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 1.14 % Allowed : 17.50 % Favored : 81.36 % Rotamer: Outliers : 4.94 % Allowed : 16.62 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.32 (0.10), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.08), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 3 349 TYR 0.018 0.003 TYR B 310 PHE 0.021 0.004 PHE X 346 HIS 0.029 0.002 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00613 (20520) covalent geometry : angle 1.03854 (27420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 331 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.3226 (OUTLIER) cc_final: 0.2455 (mmtp) REVERT: B 294 LYS cc_start: 0.4043 (OUTLIER) cc_final: 0.3520 (mmtt) REVERT: B 348 ASP cc_start: 0.5096 (m-30) cc_final: 0.4726 (t70) REVERT: E 278 ILE cc_start: 0.2120 (OUTLIER) cc_final: 0.1754 (pt) REVERT: G 353 LYS cc_start: 0.7059 (mptt) cc_final: 0.6810 (tttt) REVERT: H 347 LYS cc_start: 0.7410 (mttp) cc_final: 0.6809 (tmtp) REVERT: H 352 SER cc_start: 0.8468 (t) cc_final: 0.7791 (m) REVERT: I 281 LYS cc_start: 0.6691 (mttp) cc_final: 0.6182 (mppt) REVERT: I 294 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.5745 (tmtp) REVERT: J 288 GLN cc_start: 0.7526 (mt0) cc_final: 0.7247 (mt0) REVERT: J 352 SER cc_start: 0.8434 (t) cc_final: 0.7786 (m) REVERT: K 352 SER cc_start: 0.8294 (t) cc_final: 0.7980 (m) REVERT: L 284 LEU cc_start: 0.7160 (mp) cc_final: 0.6893 (tt) REVERT: L 352 SER cc_start: 0.8503 (t) cc_final: 0.8195 (m) REVERT: O 288 GLN cc_start: 0.8198 (mt0) cc_final: 0.7926 (tt0) REVERT: O 294 LYS cc_start: 0.7385 (tptm) cc_final: 0.6933 (mmtt) REVERT: P 279 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7571 (m110) REVERT: Q 359 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6466 (p0) REVERT: T 294 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8289 (mmtt) REVERT: T 321 LYS cc_start: 0.8250 (mttt) cc_final: 0.7938 (mtmt) REVERT: V 280 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7073 (tmtt) REVERT: Z 294 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7602 (tppp) REVERT: 0 280 LYS cc_start: 0.6924 (mtmt) cc_final: 0.6708 (mtmm) REVERT: 0 282 LEU cc_start: 0.6378 (mp) cc_final: 0.6158 (mm) REVERT: 0 294 LYS cc_start: 0.8093 (tmtt) cc_final: 0.7582 (ttmt) outliers start: 117 outliers final: 52 residues processed: 416 average time/residue: 0.8183 time to fit residues: 405.7499 Evaluate side-chains 299 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 238 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 349 ARG Chi-restraints excluded: chain I residue 278 ILE Chi-restraints excluded: chain I residue 294 LYS Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 349 ARG Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 278 ILE Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 278 ILE Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain O residue 278 ILE Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 279 ASN Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 296 ASN Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain Q residue 352 SER Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain S residue 288 GLN Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 280 LYS Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain V residue 280 LYS Chi-restraints excluded: chain V residue 359 ASN Chi-restraints excluded: chain W residue 278 ILE Chi-restraints excluded: chain W residue 280 LYS Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain W residue 330 HIS Chi-restraints excluded: chain X residue 279 ASN Chi-restraints excluded: chain X residue 344 LEU Chi-restraints excluded: chain Z residue 294 LYS Chi-restraints excluded: chain Z residue 359 ASN Chi-restraints excluded: chain 1 residue 330 HIS Chi-restraints excluded: chain 2 residue 330 HIS Chi-restraints excluded: chain 2 residue 359 ASN Chi-restraints excluded: chain 3 residue 279 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 299 HIS ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 299 HIS ** K 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 299 HIS ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 299 HIS ** M 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 299 HIS ** N 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 288 GLN ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 288 GLN ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 307 GLN ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 ASN ** 0 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 279 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5535 r_free = 0.5535 target = 0.187518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.163151 restraints weight = 78967.666| |-----------------------------------------------------------------------------| r_work (start): 0.5132 rms_B_bonded: 2.63 r_work: 0.5008 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4863 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 1.0376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20520 Z= 0.159 Angle : 0.815 9.243 27420 Z= 0.434 Chirality : 0.057 0.196 3120 Planarity : 0.007 0.087 3510 Dihedral : 8.450 55.088 2767 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 1.02 % Allowed : 14.17 % Favored : 84.81 % Rotamer: Outliers : 3.16 % Allowed : 21.43 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.29 (0.10), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.08), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 349 TYR 0.010 0.001 TYR B 310 PHE 0.016 0.003 PHE X 346 HIS 0.006 0.001 HIS W 330 Details of bonding type rmsd covalent geometry : bond 0.00367 (20520) covalent geometry : angle 0.81539 (27420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.3288 (OUTLIER) cc_final: 0.2256 (mmtp) REVERT: A 331 LYS cc_start: 0.2246 (mtpt) cc_final: 0.1190 (mttm) REVERT: B 294 LYS cc_start: 0.4280 (OUTLIER) cc_final: 0.3932 (mmtp) REVERT: D 294 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.3922 (mmtt) REVERT: G 336 GLN cc_start: 0.7691 (pt0) cc_final: 0.7467 (pt0) REVERT: H 287 VAL cc_start: 0.6140 (t) cc_final: 0.5864 (t) REVERT: H 347 LYS cc_start: 0.7636 (mttp) cc_final: 0.6788 (ttpp) REVERT: H 351 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: H 352 SER cc_start: 0.8533 (t) cc_final: 0.7887 (m) REVERT: I 294 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.5823 (tmtp) REVERT: J 288 GLN cc_start: 0.7536 (mt0) cc_final: 0.7320 (mt0) REVERT: J 351 GLN cc_start: 0.8504 (mp10) cc_final: 0.7979 (mp10) REVERT: J 352 SER cc_start: 0.8334 (t) cc_final: 0.7708 (m) REVERT: J 353 LYS cc_start: 0.7481 (mptt) cc_final: 0.6015 (tttm) REVERT: K 352 SER cc_start: 0.8243 (t) cc_final: 0.7881 (m) REVERT: L 284 LEU cc_start: 0.6812 (mp) cc_final: 0.6421 (tm) REVERT: L 342 GLU cc_start: 0.7644 (mp0) cc_final: 0.7321 (mt-10) REVERT: L 352 SER cc_start: 0.8530 (t) cc_final: 0.8212 (m) REVERT: M 288 GLN cc_start: 0.8201 (mt0) cc_final: 0.7813 (mt0) REVERT: M 352 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8152 (m) REVERT: N 321 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7913 (tttt) REVERT: P 279 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7472 (m-40) REVERT: Q 284 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7265 (tm) REVERT: Q 359 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6884 (p0) REVERT: T 280 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7101 (tmtt) REVERT: T 294 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8323 (mmtt) REVERT: T 321 LYS cc_start: 0.8167 (mttt) cc_final: 0.7786 (mtmt) REVERT: U 305 SER cc_start: 0.7264 (OUTLIER) cc_final: 0.6893 (m) REVERT: V 280 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7107 (tttt) REVERT: X 344 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6404 (mt) REVERT: Z 279 ASN cc_start: 0.7151 (OUTLIER) cc_final: 0.6851 (m-40) REVERT: Z 294 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7579 (tppp) REVERT: Z 310 TYR cc_start: 0.7156 (t80) cc_final: 0.6768 (t80) REVERT: 0 280 LYS cc_start: 0.7111 (mtmt) cc_final: 0.6898 (mtmm) REVERT: 0 294 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7596 (ttmt) outliers start: 75 outliers final: 32 residues processed: 317 average time/residue: 0.8759 time to fit residues: 328.5704 Evaluate side-chains 275 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 294 LYS Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 279 ASN Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain Q residue 284 LEU Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain S residue 293 SER Chi-restraints excluded: chain T residue 280 LYS Chi-restraints excluded: chain T residue 294 LYS Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain V residue 280 LYS Chi-restraints excluded: chain V residue 359 ASN Chi-restraints excluded: chain W residue 280 LYS Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain W residue 330 HIS Chi-restraints excluded: chain X residue 344 LEU Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Y residue 330 HIS Chi-restraints excluded: chain Z residue 279 ASN Chi-restraints excluded: chain Z residue 294 LYS Chi-restraints excluded: chain 2 residue 330 HIS Chi-restraints excluded: chain 2 residue 359 ASN Chi-restraints excluded: chain 3 residue 285 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 20 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 327 ASN E 336 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN H 327 ASN I 307 GLN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 307 GLN ** L 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 359 ASN P 279 ASN P 299 HIS R 296 ASN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 307 GLN ** W 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 ASN ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 288 GLN ** 2 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5649 r_free = 0.5649 target = 0.316584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5902 r_free = 0.5902 target = 0.284209 restraints weight = 68843.074| |-----------------------------------------------------------------------------| r_work (start): 0.5473 rms_B_bonded: 0.85 r_work: 0.5986 rms_B_bonded: 0.44 restraints_weight: 0.5000 r_work: 0.5935 rms_B_bonded: 0.80 restraints_weight: 0.2500 r_work: 0.5727 rms_B_bonded: 2.92 restraints_weight: 0.1250 r_work (final): 0.5727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 1.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 20520 Z= 0.196 Angle : 0.865 11.524 27420 Z= 0.460 Chirality : 0.058 0.435 3120 Planarity : 0.007 0.083 3510 Dihedral : 8.494 57.528 2763 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.91 % Allowed : 19.70 % Favored : 79.39 % Rotamer: Outliers : 4.43 % Allowed : 21.14 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.46 (0.10), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 349 TYR 0.012 0.002 TYR 2 310 PHE 0.014 0.003 PHE X 346 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00470 (20520) covalent geometry : angle 0.86487 (27420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 278 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.3888 (mtpt) cc_final: 0.2730 (mtpp) REVERT: B 348 ASP cc_start: 0.5412 (m-30) cc_final: 0.5138 (t70) REVERT: D 343 LYS cc_start: 0.6239 (tttt) cc_final: 0.5692 (tmtt) REVERT: H 274 LYS cc_start: 0.5194 (tptp) cc_final: 0.4908 (mttt) REVERT: H 294 LYS cc_start: 0.5825 (mppt) cc_final: 0.5563 (tptm) REVERT: H 351 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7172 (mt0) REVERT: I 305 SER cc_start: 0.8056 (t) cc_final: 0.7819 (m) REVERT: I 321 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7833 (ttmt) REVERT: J 353 LYS cc_start: 0.7366 (mptt) cc_final: 0.6961 (tttm) REVERT: O 359 ASN cc_start: 0.6151 (OUTLIER) cc_final: 0.5934 (p0) REVERT: U 305 SER cc_start: 0.6932 (OUTLIER) cc_final: 0.6483 (m) REVERT: 0 318 VAL cc_start: 0.6339 (t) cc_final: 0.6037 (t) REVERT: 2 327 ASN cc_start: 0.7283 (m-40) cc_final: 0.6974 (m-40) outliers start: 105 outliers final: 45 residues processed: 347 average time/residue: 0.8829 time to fit residues: 361.1508 Evaluate side-chains 280 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 278 ILE Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain M residue 359 ASN Chi-restraints excluded: chain N residue 312 PRO Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 278 ILE Chi-restraints excluded: chain O residue 291 CYS Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 312 PRO Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain W residue 278 ILE Chi-restraints excluded: chain W residue 280 LYS Chi-restraints excluded: chain W residue 284 LEU Chi-restraints excluded: chain X residue 351 GLN Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 2 residue 285 SER Chi-restraints excluded: chain 2 residue 330 HIS Chi-restraints excluded: chain 3 residue 285 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 167 optimal weight: 3.9990 chunk 135 optimal weight: 0.0270 chunk 104 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 336 GLN G 359 ASN J 296 ASN ** J 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 ASN P 307 GLN ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 327 ASN ** 0 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5418 r_free = 0.5418 target = 0.169143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.145393 restraints weight = 82573.072| |-----------------------------------------------------------------------------| r_work (start): 0.5068 rms_B_bonded: 2.53 r_work: 0.4959 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4818 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 1.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20520 Z= 0.193 Angle : 0.854 10.639 27420 Z= 0.455 Chirality : 0.058 0.196 3120 Planarity : 0.007 0.085 3510 Dihedral : 8.118 53.234 2743 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.83 % Allowed : 18.64 % Favored : 80.53 % Rotamer: Outliers : 3.63 % Allowed : 23.04 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.54 (0.10), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 349 TYR 0.016 0.002 TYR B 310 PHE 0.015 0.002 PHE W 346 HIS 0.007 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00439 (20520) covalent geometry : angle 0.85410 (27420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 251 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 348 ASP cc_start: 0.5538 (m-30) cc_final: 0.5298 (t70) REVERT: G 281 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6038 (mptt) REVERT: G 282 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4637 (tt) REVERT: G 322 CYS cc_start: 0.8504 (m) cc_final: 0.8258 (m) REVERT: G 352 SER cc_start: 0.8458 (t) cc_final: 0.7951 (m) REVERT: G 359 ASN cc_start: 0.5476 (OUTLIER) cc_final: 0.5227 (p0) REVERT: H 274 LYS cc_start: 0.6670 (tptp) cc_final: 0.6116 (mttt) REVERT: H 294 LYS cc_start: 0.7297 (mppt) cc_final: 0.6393 (tptm) REVERT: H 349 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7390 (tmm-80) REVERT: H 351 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: H 353 LYS cc_start: 0.7936 (mptt) cc_final: 0.7527 (ttpt) REVERT: H 356 SER cc_start: 0.8740 (t) cc_final: 0.8455 (t) REVERT: I 321 LYS cc_start: 0.8318 (ttpt) cc_final: 0.7933 (ttmt) REVERT: I 347 LYS cc_start: 0.7620 (mttp) cc_final: 0.7113 (mtpt) REVERT: J 288 GLN cc_start: 0.8094 (mt0) cc_final: 0.7610 (mt0) REVERT: K 288 GLN cc_start: 0.8321 (mt0) cc_final: 0.7838 (mt0) REVERT: K 315 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8044 (mp) REVERT: L 342 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: M 288 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: O 294 LYS cc_start: 0.7520 (tptm) cc_final: 0.6832 (mptp) REVERT: Q 359 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6351 (p0) REVERT: R 348 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: U 305 SER cc_start: 0.7486 (OUTLIER) cc_final: 0.7159 (m) REVERT: W 285 SER cc_start: 0.8006 (p) cc_final: 0.7712 (p) REVERT: X 280 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7804 (mptt) REVERT: Y 321 LYS cc_start: 0.7917 (mttt) cc_final: 0.7509 (mttp) REVERT: Y 344 LEU cc_start: 0.8057 (tt) cc_final: 0.7614 (mp) REVERT: 0 280 LYS cc_start: 0.7163 (mtmt) cc_final: 0.6963 (mtmm) REVERT: 2 317 LYS cc_start: 0.6804 (tptp) cc_final: 0.5819 (mttp) outliers start: 86 outliers final: 50 residues processed: 310 average time/residue: 0.9945 time to fit residues: 364.5709 Evaluate side-chains 284 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 223 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 359 ASN Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 296 ASN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 315 LEU Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 278 ILE Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 312 PRO Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain M residue 288 GLN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain N residue 312 PRO Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 291 CYS Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 312 PRO Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain Q residue 359 ASN Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 348 ASP Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain X residue 280 LYS Chi-restraints excluded: chain X residue 351 GLN Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Z residue 283 ASP Chi-restraints excluded: chain 0 residue 359 ASN Chi-restraints excluded: chain 2 residue 285 SER Chi-restraints excluded: chain 2 residue 359 ASN Chi-restraints excluded: chain 3 residue 285 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 221 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN H 307 GLN J 327 ASN L 327 ASN ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 288 GLN ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 336 GLN ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5383 r_free = 0.5383 target = 0.161339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.138184 restraints weight = 83885.187| |-----------------------------------------------------------------------------| r_work (start): 0.5017 rms_B_bonded: 2.49 r_work: 0.4907 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4764 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 1.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20520 Z= 0.232 Angle : 0.928 11.097 27420 Z= 0.498 Chirality : 0.060 0.231 3120 Planarity : 0.008 0.088 3510 Dihedral : 8.593 58.045 2743 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.80 % Allowed : 23.03 % Favored : 76.17 % Rotamer: Outliers : 3.50 % Allowed : 24.22 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.76 (0.09), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.38 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 349 TYR 0.019 0.002 TYR B 310 PHE 0.014 0.003 PHE X 346 HIS 0.011 0.002 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00524 (20520) covalent geometry : angle 0.92826 (27420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 253 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 286 ASN cc_start: 0.6747 (t0) cc_final: 0.5103 (m110) REVERT: F 281 LYS cc_start: 0.5477 (mttp) cc_final: 0.4925 (mppt) REVERT: F 342 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6698 (tm-30) REVERT: F 347 LYS cc_start: 0.6984 (mttp) cc_final: 0.6501 (mtpm) REVERT: F 352 SER cc_start: 0.8355 (t) cc_final: 0.7719 (m) REVERT: G 274 LYS cc_start: 0.6156 (tptp) cc_final: 0.5257 (tttt) REVERT: G 275 VAL cc_start: 0.6739 (t) cc_final: 0.5957 (t) REVERT: G 352 SER cc_start: 0.8680 (t) cc_final: 0.8121 (m) REVERT: G 353 LYS cc_start: 0.8087 (mttt) cc_final: 0.7680 (tmtt) REVERT: H 288 GLN cc_start: 0.7513 (mt0) cc_final: 0.7234 (mt0) REVERT: H 294 LYS cc_start: 0.7296 (mppt) cc_final: 0.6805 (tptm) REVERT: H 351 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7241 (mt0) REVERT: H 353 LYS cc_start: 0.8038 (mptt) cc_final: 0.7495 (ttpt) REVERT: H 356 SER cc_start: 0.9007 (t) cc_final: 0.8775 (t) REVERT: I 321 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8168 (tttt) REVERT: J 288 GLN cc_start: 0.8253 (mt0) cc_final: 0.7932 (mt0) REVERT: J 340 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8135 (mtmt) REVERT: J 349 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7604 (ttp-170) REVERT: K 342 GLU cc_start: 0.7826 (mp0) cc_final: 0.7332 (mt-10) REVERT: K 360 ILE cc_start: 0.6547 (mt) cc_final: 0.6198 (mp) REVERT: L 342 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: R 348 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: U 305 SER cc_start: 0.7503 (OUTLIER) cc_final: 0.7119 (p) REVERT: V 347 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7836 (mmtt) REVERT: W 285 SER cc_start: 0.7955 (p) cc_final: 0.7737 (p) REVERT: X 359 ASN cc_start: 0.6563 (p0) cc_final: 0.6237 (p0) REVERT: Y 321 LYS cc_start: 0.8143 (mttt) cc_final: 0.7753 (mtmm) REVERT: Y 344 LEU cc_start: 0.8386 (tt) cc_final: 0.7636 (mp) REVERT: Z 276 GLN cc_start: 0.6988 (tt0) cc_final: 0.6449 (mt0) REVERT: 2 314 ASP cc_start: 0.6696 (t0) cc_final: 0.6401 (m-30) REVERT: 2 317 LYS cc_start: 0.6764 (tptp) cc_final: 0.6100 (mttp) outliers start: 83 outliers final: 58 residues processed: 311 average time/residue: 0.8862 time to fit residues: 328.2689 Evaluate side-chains 286 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 278 ILE Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 296 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 296 ASN Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 278 ILE Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 312 PRO Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain N residue 312 PRO Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain O residue 278 ILE Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 312 PRO Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain Q residue 278 ILE Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 348 ASP Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 278 ILE Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 359 ASN Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain V residue 347 LYS Chi-restraints excluded: chain X residue 280 LYS Chi-restraints excluded: chain X residue 351 GLN Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Z residue 349 ARG Chi-restraints excluded: chain 2 residue 285 SER Chi-restraints excluded: chain 3 residue 285 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 117 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN E 279 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 GLN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 329 HIS ** 2 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5392 r_free = 0.5392 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.137398 restraints weight = 83733.841| |-----------------------------------------------------------------------------| r_work (start): 0.5026 rms_B_bonded: 2.51 r_work: 0.4917 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4773 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 1.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20520 Z= 0.189 Angle : 0.836 10.089 27420 Z= 0.448 Chirality : 0.057 0.204 3120 Planarity : 0.008 0.100 3510 Dihedral : 8.059 51.499 2743 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.76 % Allowed : 19.13 % Favored : 80.11 % Rotamer: Outliers : 2.53 % Allowed : 25.70 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.69 (0.09), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 349 TYR 0.016 0.002 TYR B 310 PHE 0.014 0.002 PHE W 346 HIS 0.005 0.001 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00423 (20520) covalent geometry : angle 0.83620 (27420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 286 ASN cc_start: 0.6319 (t0) cc_final: 0.5293 (m110) REVERT: F 277 ILE cc_start: 0.6778 (mp) cc_final: 0.6553 (mp) REVERT: F 281 LYS cc_start: 0.5744 (mttp) cc_final: 0.5187 (mppt) REVERT: F 347 LYS cc_start: 0.7192 (mttp) cc_final: 0.6498 (ttpp) REVERT: F 352 SER cc_start: 0.8222 (t) cc_final: 0.7683 (m) REVERT: G 294 LYS cc_start: 0.7673 (mmtp) cc_final: 0.6802 (tmtp) REVERT: G 321 LYS cc_start: 0.8069 (tttt) cc_final: 0.7725 (ttmt) REVERT: G 352 SER cc_start: 0.8670 (t) cc_final: 0.8168 (m) REVERT: G 353 LYS cc_start: 0.8150 (mttt) cc_final: 0.7663 (tmtt) REVERT: H 294 LYS cc_start: 0.7370 (mppt) cc_final: 0.6930 (tptm) REVERT: H 351 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7185 (mt0) REVERT: H 353 LYS cc_start: 0.8170 (mptt) cc_final: 0.7595 (tttm) REVERT: H 356 SER cc_start: 0.8962 (t) cc_final: 0.8745 (t) REVERT: I 347 LYS cc_start: 0.7669 (mttp) cc_final: 0.7132 (mtpt) REVERT: J 284 LEU cc_start: 0.6973 (mp) cc_final: 0.6764 (tt) REVERT: J 288 GLN cc_start: 0.8318 (mt0) cc_final: 0.7895 (mt0) REVERT: J 340 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8121 (mtmt) REVERT: K 342 GLU cc_start: 0.7799 (mp0) cc_final: 0.7321 (mt-10) REVERT: U 305 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7286 (p) REVERT: W 305 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7479 (t) REVERT: X 359 ASN cc_start: 0.6669 (p0) cc_final: 0.6455 (p0) REVERT: Y 276 GLN cc_start: 0.6595 (tt0) cc_final: 0.6196 (mt0) REVERT: Y 284 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6604 (mm) REVERT: Y 321 LYS cc_start: 0.8183 (mttt) cc_final: 0.7864 (mtmm) REVERT: Z 276 GLN cc_start: 0.6911 (tt0) cc_final: 0.6386 (mt0) REVERT: 1 346 PHE cc_start: 0.7124 (m-80) cc_final: 0.6886 (m-80) REVERT: 2 314 ASP cc_start: 0.6932 (t0) cc_final: 0.6581 (m-30) REVERT: 2 317 LYS cc_start: 0.6687 (tptp) cc_final: 0.6315 (mttp) outliers start: 60 outliers final: 45 residues processed: 281 average time/residue: 0.9297 time to fit residues: 307.4204 Evaluate side-chains 263 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 296 ASN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 283 ASP Chi-restraints excluded: chain K residue 319 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 312 PRO Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain N residue 312 PRO Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 347 LYS Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 356 SER Chi-restraints excluded: chain O residue 291 CYS Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain P residue 293 SER Chi-restraints excluded: chain P residue 312 PRO Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain T residue 278 ILE Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain X residue 280 LYS Chi-restraints excluded: chain X residue 351 GLN Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Z residue 349 ARG Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 2 residue 285 SER Chi-restraints excluded: chain 3 residue 285 SER Chi-restraints excluded: chain 3 residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 37 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 198 optimal weight: 0.1980 chunk 195 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 307 GLN I 276 GLN K 336 GLN ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 279 ASN ** 2 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5431 r_free = 0.5431 target = 0.162813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.139564 restraints weight = 82711.749| |-----------------------------------------------------------------------------| r_work (start): 0.5066 rms_B_bonded: 2.53 r_work: 0.4957 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4813 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 1.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20520 Z= 0.134 Angle : 0.766 11.869 27420 Z= 0.401 Chirality : 0.055 0.172 3120 Planarity : 0.007 0.087 3510 Dihedral : 7.315 52.127 2743 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.76 % Allowed : 16.86 % Favored : 82.39 % Rotamer: Outliers : 1.48 % Allowed : 27.22 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.49 (0.09), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 349 TYR 0.010 0.001 TYR Y 310 PHE 0.014 0.002 PHE 1 346 HIS 0.005 0.001 HIS W 330 Details of bonding type rmsd covalent geometry : bond 0.00303 (20520) covalent geometry : angle 0.76605 (27420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 274 LYS cc_start: 0.5069 (OUTLIER) cc_final: 0.3624 (mtpt) REVERT: E 286 ASN cc_start: 0.6197 (t0) cc_final: 0.5380 (m110) REVERT: F 281 LYS cc_start: 0.5519 (mttp) cc_final: 0.5202 (mppt) REVERT: F 347 LYS cc_start: 0.7306 (mttp) cc_final: 0.6540 (ttpp) REVERT: F 352 SER cc_start: 0.8126 (t) cc_final: 0.7670 (m) REVERT: G 294 LYS cc_start: 0.7720 (mmtp) cc_final: 0.6660 (tptm) REVERT: G 352 SER cc_start: 0.8560 (t) cc_final: 0.8165 (m) REVERT: G 353 LYS cc_start: 0.8076 (mttt) cc_final: 0.7660 (tmtt) REVERT: H 294 LYS cc_start: 0.7346 (mppt) cc_final: 0.6644 (tptm) REVERT: H 351 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: I 347 LYS cc_start: 0.7568 (mttp) cc_final: 0.7058 (mtpt) REVERT: J 284 LEU cc_start: 0.6895 (mp) cc_final: 0.6636 (tt) REVERT: J 340 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8098 (mtmt) REVERT: K 284 LEU cc_start: 0.6987 (mp) cc_final: 0.6660 (tt) REVERT: K 288 GLN cc_start: 0.8370 (mt0) cc_final: 0.7987 (mt0) REVERT: K 342 GLU cc_start: 0.7800 (mp0) cc_final: 0.7291 (mt-10) REVERT: L 347 LYS cc_start: 0.7901 (mptt) cc_final: 0.7655 (mptt) REVERT: O 294 LYS cc_start: 0.7656 (tmtm) cc_final: 0.6742 (mmtp) REVERT: W 282 LEU cc_start: 0.7383 (mp) cc_final: 0.7153 (tt) REVERT: Y 276 GLN cc_start: 0.6590 (tt0) cc_final: 0.6185 (mt0) REVERT: Y 280 LYS cc_start: 0.7066 (mmtt) cc_final: 0.6513 (mppt) REVERT: Y 284 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6663 (mm) REVERT: Y 321 LYS cc_start: 0.8089 (mttt) cc_final: 0.7654 (mmtp) REVERT: Z 276 GLN cc_start: 0.6840 (tt0) cc_final: 0.6363 (mt0) REVERT: 2 314 ASP cc_start: 0.6792 (t0) cc_final: 0.6559 (m-30) REVERT: 3 314 ASP cc_start: 0.5338 (OUTLIER) cc_final: 0.5122 (p0) outliers start: 35 outliers final: 28 residues processed: 250 average time/residue: 0.8715 time to fit residues: 258.9994 Evaluate side-chains 228 residues out of total 2370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 319 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain L residue 291 CYS Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 319 THR Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain N residue 312 PRO Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 349 ARG Chi-restraints excluded: chain P residue 312 PRO Chi-restraints excluded: chain P residue 320 SER Chi-restraints excluded: chain S residue 278 ILE Chi-restraints excluded: chain T residue 348 ASP Chi-restraints excluded: chain U residue 293 SER Chi-restraints excluded: chain V residue 320 SER Chi-restraints excluded: chain X residue 351 GLN Chi-restraints excluded: chain Y residue 284 LEU Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Z residue 349 ARG Chi-restraints excluded: chain 1 residue 316 SER Chi-restraints excluded: chain 1 residue 319 THR Chi-restraints excluded: chain 2 residue 285 SER Chi-restraints excluded: chain 3 residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 201 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** O 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 336 GLN ** W 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5467 r_free = 0.5467 target = 0.164573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.142681 restraints weight = 81800.566| |-----------------------------------------------------------------------------| r_work (start): 0.5008 rms_B_bonded: 2.46 r_work: 0.4887 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4743 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 1.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20520 Z= 0.148 Angle : 0.770 11.177 27420 Z= 0.407 Chirality : 0.056 0.178 3120 Planarity : 0.007 0.076 3510 Dihedral : 7.393 50.653 2743 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.72 % Allowed : 17.61 % Favored : 81.67 % Rotamer: Outliers : 1.77 % Allowed : 27.76 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.48 (0.09), residues: 2640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.17 (0.07), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 349 TYR 0.012 0.001 TYR B 310 PHE 0.015 0.002 PHE 0 346 HIS 0.008 0.001 HIS W 330 Details of bonding type rmsd covalent geometry : bond 0.00337 (20520) covalent geometry : angle 0.76982 (27420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11944.84 seconds wall clock time: 203 minutes 48.03 seconds (12228.03 seconds total)