Starting phenix.real_space_refine on Sun Sep 13 05:44:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.map" model { file = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fli_29279/09_2026/8fli_29279.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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: 6 Type Number sf(0) Gaussians P 828 5.49 5 Mg 3 5.21 5 S 8 5.16 5 C 10319 2.51 5 N 3961 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21511 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 828, 17751 Classifications: {'RNAv2': 828} Modifications used: {'rna2p_pur': 65, 'rna2p_pyr': 43, 'rna3p_pur': 400, 'rna3p_pyr': 320} Link IDs: {'rna2p': 108, 'rna3p': 719} Chain breaks: 2 Chain: "B" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3757 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 17, 'TRANS': 440} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.15, per 1000 atoms: 0.19 Number of scatterers: 21511 At special positions: 0 Unit cell: (117.3, 158.7, 238.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 828 15.00 Mg 3 11.99 O 6392 8.00 N 3961 7.00 C 10319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 337.6 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 858 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 38.9% alpha, 7.2% beta 211 base pairs and 351 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.706A pdb=" N ILE B 26 " --> pdb=" O TRP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 removed outlier: 3.612A pdb=" N ALA B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 32 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 5.088A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 77 removed outlier: 3.608A pdb=" N ALA B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.966A pdb=" N LYS B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.652A pdb=" N MET B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.171A pdb=" N ALA B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.568A pdb=" N ILE B 200 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.634A pdb=" N ALA B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.597A pdb=" N HIS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.751A pdb=" N GLN B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 5.282A pdb=" N ALA B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 378 Proline residue: B 370 - end of helix removed outlier: 3.571A pdb=" N LYS B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 374 " --> pdb=" O PRO B 370 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.586A pdb=" N ASN B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 removed outlier: 4.565A pdb=" N LYS B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 419 Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.847A pdb=" N ARG B 115 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 131 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 117 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 129 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 119 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 127 " --> pdb=" O ILE B 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272 removed outlier: 3.804A pdb=" N TYR B 187 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.562A pdb=" N PHE B 319 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 326 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 327 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 334 " --> pdb=" O ARG B 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 420 through 421 removed outlier: 3.503A pdb=" N THR B 432 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 444 " --> pdb=" O THR B 432 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 255 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 544 hydrogen bonds 932 hydrogen bond angles 0 basepair planarities 211 basepair parallelities 351 stacking parallelities Total time for adding SS restraints: 6.03 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2711 1.33 - 1.45: 10877 1.45 - 1.57: 8463 1.57 - 1.69: 1653 1.69 - 1.81: 12 Bond restraints: 23716 Sorted by residual: bond pdb=" N TYR B 419 " pdb=" CA TYR B 419 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.16e-02 7.43e+03 1.12e+01 bond pdb=" CA HIS B 397 " pdb=" C HIS B 397 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.72e-02 3.38e+03 9.16e+00 bond pdb=" C THR B 415 " pdb=" O THR B 415 " ideal model delta sigma weight residual 1.235 1.271 -0.035 1.26e-02 6.30e+03 7.90e+00 bond pdb=" C LYS B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.328 1.357 -0.029 1.25e-02 6.40e+03 5.40e+00 bond pdb=" N TRP B 414 " pdb=" CA TRP B 414 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 36003 4.64 - 9.28: 164 9.28 - 13.92: 1 13.92 - 18.56: 1 18.56 - 23.20: 1 Bond angle restraints: 36170 Sorted by residual: angle pdb=" O3' U A 859 " pdb=" C3' U A 859 " pdb=" C2' U A 859 " ideal model delta sigma weight residual 113.80 90.60 23.20 3.00e+00 1.11e-01 5.98e+01 angle pdb=" C3' G A 840 " pdb=" O3' G A 840 " pdb=" P G A 841 " ideal model delta sigma weight residual 119.70 126.84 -7.14 1.20e+00 6.94e-01 3.54e+01 angle pdb=" C3' U A 859 " pdb=" O3' U A 859 " pdb=" P A A 860 " ideal model delta sigma weight residual 119.70 125.70 -6.00 1.20e+00 6.94e-01 2.50e+01 angle pdb=" C LYS B 418 " pdb=" N TYR B 419 " pdb=" CA TYR B 419 " ideal model delta sigma weight residual 122.67 114.94 7.73 1.59e+00 3.96e-01 2.36e+01 angle pdb=" C4' U A 859 " pdb=" C3' U A 859 " pdb=" O3' U A 859 " ideal model delta sigma weight residual 112.50 126.61 -14.11 3.00e+00 1.11e-01 2.21e+01 ... (remaining 36165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 11537 35.51 - 71.03: 2792 71.03 - 106.54: 322 106.54 - 142.05: 2 142.05 - 177.57: 5 Dihedral angle restraints: 14658 sinusoidal: 13331 harmonic: 1327 Sorted by residual: dihedral pdb=" C4' A A 715 " pdb=" C3' A A 715 " pdb=" C2' A A 715 " pdb=" C1' A A 715 " ideal model delta sinusoidal sigma weight residual 36.34 -39.13 75.47 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' C A 846 " pdb=" C3' C A 846 " pdb=" C2' C A 846 " pdb=" C1' C A 846 " ideal model delta sinusoidal sigma weight residual 36.34 -38.55 74.90 1 3.10e+00 1.04e-01 7.39e+02 dihedral pdb=" C4' A A 401 " pdb=" C3' A A 401 " pdb=" C2' A A 401 " pdb=" C1' A A 401 " ideal model delta sinusoidal sigma weight residual 36.34 -38.11 74.45 1 3.10e+00 1.04e-01 7.31e+02 ... (remaining 14655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3563 0.101 - 0.202: 211 0.202 - 0.303: 901 0.303 - 0.404: 7 0.404 - 0.505: 5 Chirality restraints: 4687 Sorted by residual: chirality pdb=" P G A 828 " pdb=" OP1 G A 828 " pdb=" OP2 G A 828 " pdb=" O5' G A 828 " both_signs ideal model delta sigma weight residual True 2.17 -2.68 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" P G A 830 " pdb=" OP1 G A 830 " pdb=" OP2 G A 830 " pdb=" O5' G A 830 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" P G A 829 " pdb=" OP1 G A 829 " pdb=" OP2 G A 829 " pdb=" O5' G A 829 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 4684 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 305 " 0.025 2.00e-02 2.50e+03 2.79e-02 1.75e+01 pdb=" N1 C A 305 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C A 305 " 0.054 2.00e-02 2.50e+03 pdb=" O2 C A 305 " -0.032 2.00e-02 2.50e+03 pdb=" N3 C A 305 " -0.016 2.00e-02 2.50e+03 pdb=" C4 C A 305 " 0.026 2.00e-02 2.50e+03 pdb=" N4 C A 305 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C A 305 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 305 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 112 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO B 113 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 410 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS B 410 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 410 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO B 411 " 0.019 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 16 2.19 - 2.86: 7122 2.86 - 3.54: 33277 3.54 - 4.22: 64014 4.22 - 4.90: 81169 Nonbonded interactions: 185598 Sorted by model distance: nonbonded pdb=" OE1 GLU B 470 " pdb=" CD1 TRP B 471 " model vdw 1.508 3.260 nonbonded pdb=" O3' G A 0 " pdb="MG MG A 903 " model vdw 1.862 2.170 nonbonded pdb=" OP2 U A 1 " pdb="MG MG A 903 " model vdw 1.895 2.170 nonbonded pdb=" OP1 A A 6 " pdb="MG MG A 901 " model vdw 1.901 2.170 nonbonded pdb=" O LYS B 348 " pdb=" OD1 ASP B 351 " model vdw 1.923 3.040 ... (remaining 185593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 0.040 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.490 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.005 0.055 23716 Z= 0.262 Angle : 1.029 23.197 36170 Z= 0.419 Chirality : 0.115 0.505 4687 Planarity : 0.005 0.088 1481 Dihedral : 28.795 177.569 13800 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.45 % Favored : 82.89 % Rotamer: Outliers : 0.26 % Allowed : 41.33 % Favored : 58.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.36), residues: 456 helix: -2.28 (0.36), residues: 188 sheet: -1.99 (0.88), residues: 38 loop : -2.69 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 401 TYR 0.016 0.002 TYR B 66 PHE 0.013 0.002 PHE B 430 TRP 0.016 0.002 TRP B 471 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (23716) covalent geometry : angle 1.02879 / 0.42 (36170) hydrogen bonds : bond 0.14094 / 7.48 ( 636) hydrogen bonds : angle 5.71795 / 2.25 ( 1187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.318 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1502 time to fit residues: 8.3281 Evaluate side-chains 35 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.095343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067623 restraints weight = 86331.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069463 restraints weight = 38645.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070634 restraints weight = 26092.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071300 restraints weight = 21568.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071551 restraints weight = 19593.618| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23716 Z= 0.326 Angle : 1.467 21.097 36170 Z= 0.569 Chirality : 0.114 1.392 4687 Planarity : 0.006 0.087 1481 Dihedral : 26.912 176.236 12845 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 6.38 % Allowed : 37.76 % Favored : 55.87 % 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 are not related in a simple way. whole: -3.54 (0.36), residues: 456 helix: -2.11 (0.37), residues: 182 sheet: -2.12 (0.86), residues: 38 loop : -2.60 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 105 TYR 0.014 0.002 TYR B 419 PHE 0.015 0.002 PHE B 430 TRP 0.012 0.002 TRP B 402 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.33 (23716) covalent geometry : angle 1.46700 / 0.57 (36170) hydrogen bonds : bond 0.09519 / 4.89 ( 636) hydrogen bonds : angle 3.35025 / 1.37 ( 1187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 35 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 GLN cc_start: 0.8000 (pm20) cc_final: 0.7571 (pm20) outliers start: 25 outliers final: 14 residues processed: 56 average time/residue: 0.1505 time to fit residues: 13.0532 Evaluate side-chains 50 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 chunk 102 optimal weight: 0.4980 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.070426 restraints weight = 85893.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072487 restraints weight = 37072.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.073785 restraints weight = 24680.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074392 restraints weight = 20200.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.074738 restraints weight = 18332.576| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23716 Z= 0.202 Angle : 1.192 15.626 36170 Z= 0.461 Chirality : 0.090 1.047 4687 Planarity : 0.005 0.086 1481 Dihedral : 26.647 179.119 12843 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.47 % Favored : 84.87 % Rotamer: Outliers : 6.38 % Allowed : 35.97 % Favored : 57.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.37), residues: 456 helix: -1.83 (0.36), residues: 191 sheet: -2.07 (0.84), residues: 36 loop : -2.38 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 105 TYR 0.017 0.001 TYR B 66 PHE 0.009 0.001 PHE B 321 TRP 0.015 0.001 TRP B 226 HIS 0.004 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (23716) covalent geometry : angle 1.19181 / 0.46 (36170) hydrogen bonds : bond 0.08399 / 4.48 ( 636) hydrogen bonds : angle 2.91015 / 1.19 ( 1187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8289 (mtm-85) REVERT: B 226 TRP cc_start: 0.7366 (t60) cc_final: 0.7038 (t60) REVERT: B 228 GLN cc_start: 0.7946 (pm20) cc_final: 0.7652 (pm20) REVERT: B 438 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7690 (pp20) outliers start: 25 outliers final: 16 residues processed: 65 average time/residue: 0.1379 time to fit residues: 14.0192 Evaluate side-chains 57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.093246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065398 restraints weight = 87813.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067287 restraints weight = 39408.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068499 restraints weight = 26987.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069171 restraints weight = 22350.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069438 restraints weight = 20267.813| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 23716 Z= 0.378 Angle : 1.412 19.190 36170 Z= 0.547 Chirality : 0.101 0.873 4687 Planarity : 0.006 0.089 1481 Dihedral : 26.825 179.137 12843 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.66 % Allowed : 18.64 % Favored : 80.70 % Rotamer: Outliers : 10.20 % Allowed : 33.67 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.35), residues: 456 helix: -2.01 (0.36), residues: 182 sheet: -2.15 (1.07), residues: 24 loop : -2.63 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 478 TYR 0.014 0.002 TYR B 66 PHE 0.037 0.003 PHE B 321 TRP 0.020 0.002 TRP B 402 HIS 0.010 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.38 (23716) covalent geometry : angle 1.41242 / 0.55 (36170) hydrogen bonds : bond 0.10212 / 5.25 ( 636) hydrogen bonds : angle 3.40871 / 1.40 ( 1187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 36 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7419 (t80) REVERT: B 228 GLN cc_start: 0.8221 (pm20) cc_final: 0.7704 (pm20) REVERT: B 390 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.7467 (tmm-80) REVERT: B 432 THR cc_start: 0.9654 (OUTLIER) cc_final: 0.9335 (p) REVERT: B 438 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8079 (pp20) REVERT: B 448 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8495 (tmtt) outliers start: 40 outliers final: 26 residues processed: 72 average time/residue: 0.1778 time to fit residues: 19.0546 Evaluate side-chains 64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 33 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 109 TYR Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 0.0040 chunk 98 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.099184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072115 restraints weight = 85657.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074191 restraints weight = 36681.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075480 restraints weight = 24362.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.076182 restraints weight = 19867.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076480 restraints weight = 17869.514| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23716 Z= 0.157 Angle : 1.111 15.335 36170 Z= 0.431 Chirality : 0.084 0.967 4687 Planarity : 0.005 0.087 1481 Dihedral : 26.439 178.588 12843 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.25 % Favored : 85.09 % Rotamer: Outliers : 5.36 % Allowed : 38.52 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.37), residues: 456 helix: -1.57 (0.37), residues: 190 sheet: -2.03 (0.83), residues: 37 loop : -2.28 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 401 TYR 0.022 0.001 TYR B 66 PHE 0.015 0.002 PHE B 321 TRP 0.019 0.002 TRP B 226 HIS 0.004 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (23716) covalent geometry : angle 1.11115 / 0.43 (36170) hydrogen bonds : bond 0.08176 / 4.36 ( 636) hydrogen bonds : angle 2.74707 / 1.12 ( 1187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: B 226 TRP cc_start: 0.7311 (t60) cc_final: 0.6999 (t60) REVERT: B 228 GLN cc_start: 0.7955 (pm20) cc_final: 0.7653 (pm20) outliers start: 21 outliers final: 15 residues processed: 57 average time/residue: 0.1536 time to fit residues: 13.9576 Evaluate side-chains 55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.095167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067660 restraints weight = 87265.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069564 restraints weight = 39640.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070752 restraints weight = 27109.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071416 restraints weight = 22497.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071649 restraints weight = 20429.034| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 23716 Z= 0.289 Angle : 1.254 16.687 36170 Z= 0.485 Chirality : 0.091 0.885 4687 Planarity : 0.006 0.089 1481 Dihedral : 26.569 177.908 12843 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 7.91 % Allowed : 37.76 % Favored : 54.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.37), residues: 456 helix: -1.60 (0.37), residues: 183 sheet: -2.30 (1.06), residues: 25 loop : -2.28 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 440 TYR 0.013 0.002 TYR B 66 PHE 0.015 0.002 PHE B 297 TRP 0.014 0.002 TRP B 59 HIS 0.006 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.29 (23716) covalent geometry : angle 1.25430 / 0.49 (36170) hydrogen bonds : bond 0.08929 / 4.64 ( 636) hydrogen bonds : angle 3.06111 / 1.25 ( 1187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 38 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8206 (mtm-85) REVERT: B 226 TRP cc_start: 0.7384 (t60) cc_final: 0.6982 (t60) REVERT: B 228 GLN cc_start: 0.8065 (pm20) cc_final: 0.7693 (pm20) REVERT: B 390 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7437 (tmm-80) REVERT: B 432 THR cc_start: 0.9642 (OUTLIER) cc_final: 0.9328 (p) outliers start: 31 outliers final: 21 residues processed: 65 average time/residue: 0.1669 time to fit residues: 16.6324 Evaluate side-chains 61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 37 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 113 optimal weight: 0.4980 chunk 110 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.097926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.070664 restraints weight = 86544.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072743 restraints weight = 36199.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.074029 restraints weight = 23912.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.074737 restraints weight = 19511.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075001 restraints weight = 17560.934| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23716 Z= 0.182 Angle : 1.123 14.489 36170 Z= 0.435 Chirality : 0.084 0.887 4687 Planarity : 0.005 0.089 1481 Dihedral : 26.437 179.039 12843 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.69 % Favored : 84.65 % Rotamer: Outliers : 5.87 % Allowed : 39.03 % Favored : 55.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.38), residues: 456 helix: -1.39 (0.38), residues: 189 sheet: -1.70 (1.05), residues: 23 loop : -2.21 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 401 TYR 0.018 0.001 TYR B 66 PHE 0.010 0.001 PHE B 321 TRP 0.014 0.002 TRP B 226 HIS 0.003 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (23716) covalent geometry : angle 1.12286 / 0.44 (36170) hydrogen bonds : bond 0.08141 / 4.31 ( 636) hydrogen bonds : angle 2.78436 / 1.13 ( 1187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 TRP cc_start: 0.7337 (t60) cc_final: 0.7028 (t60) REVERT: B 228 GLN cc_start: 0.7900 (pm20) cc_final: 0.7543 (pm20) REVERT: B 390 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7339 (tmm-80) REVERT: B 432 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9319 (p) outliers start: 23 outliers final: 18 residues processed: 58 average time/residue: 0.1671 time to fit residues: 15.0744 Evaluate side-chains 58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 121 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 126 optimal weight: 0.0870 chunk 124 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.098145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.070891 restraints weight = 86436.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072990 restraints weight = 36154.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074204 restraints weight = 23869.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074935 restraints weight = 19628.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.075278 restraints weight = 17659.906| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23716 Z= 0.170 Angle : 1.116 14.520 36170 Z= 0.433 Chirality : 0.084 0.885 4687 Planarity : 0.006 0.089 1481 Dihedral : 26.431 178.736 12843 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.91 % Favored : 84.43 % Rotamer: Outliers : 6.12 % Allowed : 38.27 % Favored : 55.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.38), residues: 456 helix: -1.35 (0.38), residues: 189 sheet: -1.66 (1.05), residues: 23 loop : -2.12 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 401 TYR 0.018 0.001 TYR B 66 PHE 0.009 0.001 PHE B 321 TRP 0.015 0.001 TRP B 226 HIS 0.004 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (23716) covalent geometry : angle 1.11629 / 0.43 (36170) hydrogen bonds : bond 0.08002 / 4.24 ( 636) hydrogen bonds : angle 2.75211 / 1.12 ( 1187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 TRP cc_start: 0.7328 (t60) cc_final: 0.6996 (t60) REVERT: B 228 GLN cc_start: 0.7838 (pm20) cc_final: 0.7506 (pm20) REVERT: B 328 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: B 390 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.7338 (tmm-80) REVERT: B 401 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7572 (ttm110) REVERT: B 432 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9320 (p) outliers start: 24 outliers final: 17 residues processed: 61 average time/residue: 0.1591 time to fit residues: 15.1204 Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.094582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067123 restraints weight = 86964.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069009 restraints weight = 39078.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070209 restraints weight = 26727.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.070831 restraints weight = 22133.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071110 restraints weight = 20129.093| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 23716 Z= 0.325 Angle : 1.289 16.715 36170 Z= 0.500 Chirality : 0.093 0.826 4687 Planarity : 0.006 0.092 1481 Dihedral : 26.563 179.443 12843 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 8.16 % Allowed : 36.48 % Favored : 55.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.37), residues: 456 helix: -1.66 (0.36), residues: 189 sheet: -2.17 (1.04), residues: 25 loop : -2.28 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 401 TYR 0.016 0.002 TYR B 66 PHE 0.015 0.002 PHE B 430 TRP 0.018 0.002 TRP B 59 HIS 0.006 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.32 (23716) covalent geometry : angle 1.28943 / 0.50 (36170) hydrogen bonds : bond 0.09032 / 4.71 ( 636) hydrogen bonds : angle 3.13058 / 1.27 ( 1187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 35 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8260 (mtm-85) REVERT: B 129 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8737 (mm) REVERT: B 226 TRP cc_start: 0.7416 (t60) cc_final: 0.7049 (t60) REVERT: B 228 GLN cc_start: 0.8105 (pm20) cc_final: 0.7822 (pm20) REVERT: B 328 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8102 (mtmm) REVERT: B 390 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7454 (tmm-80) REVERT: B 432 THR cc_start: 0.9652 (OUTLIER) cc_final: 0.9328 (p) REVERT: B 448 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8480 (tmtt) REVERT: B 471 TRP cc_start: 0.8196 (m-10) cc_final: 0.7935 (m-10) outliers start: 32 outliers final: 22 residues processed: 63 average time/residue: 0.1705 time to fit residues: 16.4219 Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 35 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 427 HIS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 109 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.101369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.074519 restraints weight = 86160.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076676 restraints weight = 35498.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.078039 restraints weight = 23195.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.078732 restraints weight = 18695.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079077 restraints weight = 16755.393| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23716 Z= 0.142 Angle : 1.067 15.081 36170 Z= 0.413 Chirality : 0.080 0.832 4687 Planarity : 0.005 0.091 1481 Dihedral : 26.255 179.721 12843 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.04 % Favored : 85.31 % Rotamer: Outliers : 3.83 % Allowed : 40.31 % Favored : 55.87 % 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 are not related in a simple way. whole: -2.63 (0.38), residues: 456 helix: -1.34 (0.38), residues: 190 sheet: -1.78 (0.80), residues: 36 loop : -2.08 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 401 TYR 0.020 0.001 TYR B 66 PHE 0.009 0.001 PHE B 321 TRP 0.015 0.001 TRP B 226 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (23716) covalent geometry : angle 1.06734 / 0.41 (36170) hydrogen bonds : bond 0.08017 / 4.30 ( 636) hydrogen bonds : angle 2.63857 / 1.07 ( 1187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 GLU cc_start: 0.8988 (tp30) cc_final: 0.8758 (tt0) REVERT: B 432 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9234 (p) REVERT: B 448 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8327 (tmtt) outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 0.1693 time to fit residues: 14.5221 Evaluate side-chains 53 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 107 optimal weight: 0.2980 chunk 78 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 174 GLN ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.095850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.068488 restraints weight = 86310.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070428 restraints weight = 37133.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.071620 restraints weight = 24718.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.072285 restraints weight = 20290.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072631 restraints weight = 18351.270| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23716 Z= 0.291 Angle : 1.226 15.656 36170 Z= 0.475 Chirality : 0.089 0.765 4687 Planarity : 0.006 0.094 1481 Dihedral : 26.437 179.111 12843 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 4.08 % Allowed : 41.33 % Favored : 54.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.38), residues: 456 helix: -1.57 (0.37), residues: 189 sheet: -1.61 (1.07), residues: 23 loop : -2.18 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 478 TYR 0.018 0.002 TYR B 66 PHE 0.012 0.002 PHE B 430 TRP 0.017 0.002 TRP B 402 HIS 0.007 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.29 (23716) covalent geometry : angle 1.22632 / 0.48 (36170) hydrogen bonds : bond 0.08596 / 4.52 ( 636) hydrogen bonds : angle 3.01040 / 1.21 ( 1187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4158.38 seconds wall clock time: 72 minutes 53.60 seconds (4373.60 seconds total)