Starting phenix.real_space_refine on Sat Jul 4 13:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fli_29279/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.map" model { file = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_2026/8fli_29279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fli_29279/07_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-dev-6108/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: {'RNA': 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: 3.49, per 1000 atoms: 0.16 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: 1.53 Conformation dependent library (CDL) restraints added in 270.8 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: 2.82 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: 4.97 Time building geometry restraints manager: 2.15 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 - 4.62: 36125 4.62 - 9.24: 42 9.24 - 13.86: 2 13.86 - 18.48: 0 18.48 - 23.10: 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 113.70 90.60 23.10 1.50e+00 4.44e-01 2.37e+02 angle pdb=" C4' U A 859 " pdb=" C3' U A 859 " pdb=" O3' U A 859 " ideal model delta sigma weight residual 113.00 126.61 -13.61 1.50e+00 4.44e-01 8.23e+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=" C3' G A 840 " pdb=" O3' G A 840 " pdb=" P G A 841 " ideal model delta sigma weight residual 120.20 126.84 -6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" C4' U A 825 " pdb=" C3' U A 825 " pdb=" O3' U A 825 " ideal model delta sigma weight residual 113.00 106.42 6.58 1.50e+00 4.44e-01 1.92e+01 ... (remaining 36165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 12421 35.51 - 71.03: 1923 71.03 - 106.54: 298 106.54 - 142.06: 8 142.06 - 177.57: 8 Dihedral angle restraints: 14658 sinusoidal: 13331 harmonic: 1327 Sorted by residual: dihedral pdb=" O4' U A 595 " pdb=" C1' U A 595 " pdb=" N1 U A 595 " pdb=" C2 U A 595 " ideal model delta sinusoidal sigma weight residual 200.00 41.16 158.84 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' C A -6 " pdb=" C1' C A -6 " pdb=" N1 C A -6 " pdb=" C2 C A -6 " ideal model delta sinusoidal sigma weight residual 200.00 50.66 149.34 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U A 498 " pdb=" C1' U A 498 " pdb=" N1 U A 498 " pdb=" C2 U A 498 " ideal model delta sinusoidal sigma weight residual 232.00 56.66 175.34 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 14655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4201 0.054 - 0.107: 409 0.107 - 0.161: 53 0.161 - 0.215: 16 0.215 - 0.268: 8 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 2.41 -2.68 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1' G A 531 " pdb=" O4' G A 531 " pdb=" C2' G A 531 " pdb=" N9 G A 531 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1' A A 630 " pdb=" O4' A A 630 " pdb=" C2' A A 630 " pdb=" N9 A A 630 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.33e+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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- 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= 0.250 Angle : 0.680 23.097 36170 Z= 0.356 Chirality : 0.036 0.268 4687 Planarity : 0.005 0.088 1481 Dihedral : 25.572 177.569 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 0.00477 / 0.25 (23716) covalent geometry : angle 0.68039 / 0.36 (36170) hydrogen bonds : bond 0.14094 / 8.66 ( 636) hydrogen bonds : angle 5.71795 / 3.15 ( 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 : 0.322 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1574 time to fit residues: 8.6000 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 : 0.357 ------------------------------------------------------------------------------- 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: 5.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.093940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.066047 restraints weight = 85005.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068003 restraints weight = 36260.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069227 restraints weight = 24300.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069827 restraints weight = 19984.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070135 restraints weight = 18119.864| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 23716 Z= 0.297 Angle : 0.753 12.841 36170 Z= 0.369 Chirality : 0.037 0.252 4687 Planarity : 0.006 0.087 1481 Dihedral : 25.582 175.170 12845 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 6.38 % Allowed : 38.27 % 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: -3.60 (0.35), residues: 456 helix: -2.16 (0.36), residues: 182 sheet: -2.24 (1.10), residues: 24 loop : -2.64 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.016 0.002 TYR B 66 PHE 0.015 0.002 PHE B 430 TRP 0.014 0.002 TRP B 471 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.30 (23716) covalent geometry : angle 0.75254 / 0.37 (36170) hydrogen bonds : bond 0.08447 / 5.13 ( 636) hydrogen bonds : angle 3.27396 / 1.89 ( 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 62 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 228 GLN cc_start: 0.8047 (pm20) cc_final: 0.7600 (pm20) REVERT: B 417 ASN cc_start: 0.9094 (t0) cc_final: 0.8891 (t0) REVERT: B 471 TRP cc_start: 0.7005 (m-10) cc_final: 0.6781 (m-10) outliers start: 25 outliers final: 15 residues processed: 58 average time/residue: 0.1487 time to fit residues: 13.2479 Evaluate side-chains 51 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 249 ASN 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: 20.0000 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 67 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 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 = 0.3744 r_free = 0.3744 target = 0.095151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067572 restraints weight = 84225.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.069548 restraints weight = 34519.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070753 restraints weight = 22627.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071423 restraints weight = 18443.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071717 restraints weight = 16634.586| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23716 Z= 0.202 Angle : 0.637 13.066 36170 Z= 0.318 Chirality : 0.033 0.273 4687 Planarity : 0.005 0.087 1481 Dihedral : 25.377 172.365 12843 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.35 % Favored : 83.99 % Rotamer: Outliers : 7.91 % Allowed : 35.97 % 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: -3.29 (0.36), residues: 456 helix: -1.88 (0.37), residues: 184 sheet: -2.03 (0.85), residues: 36 loop : -2.47 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 105 TYR 0.019 0.001 TYR B 66 PHE 0.011 0.002 PHE B 321 TRP 0.016 0.002 TRP B 226 HIS 0.007 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (23716) covalent geometry : angle 0.63708 / 0.32 (36170) hydrogen bonds : bond 0.07056 / 4.23 ( 636) hydrogen bonds : angle 2.92658 / 1.67 ( 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 70 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 39 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8258 (mtm-85) REVERT: B 226 TRP cc_start: 0.7398 (t60) cc_final: 0.7087 (t60) REVERT: B 228 GLN cc_start: 0.7945 (pm20) cc_final: 0.7572 (pm20) REVERT: B 260 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8050 (ptmt) REVERT: B 390 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.7712 (tmm-80) REVERT: B 438 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7743 (pp20) outliers start: 31 outliers final: 18 residues processed: 65 average time/residue: 0.1670 time to fit residues: 16.0301 Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 38 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 242 VAL Chi-restraints excluded: chain B residue 260 LYS 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 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 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: 7.9990 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.091087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063340 restraints weight = 88112.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065174 restraints weight = 38576.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066313 restraints weight = 26259.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066937 restraints weight = 21789.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067188 restraints weight = 19827.267| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 23716 Z= 0.437 Angle : 0.932 12.896 36170 Z= 0.451 Chirality : 0.045 0.302 4687 Planarity : 0.007 0.093 1481 Dihedral : 25.856 175.422 12843 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.66 % Allowed : 18.86 % Favored : 80.48 % Rotamer: Outliers : 11.22 % Allowed : 33.42 % 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: -3.85 (0.35), residues: 456 helix: -2.22 (0.35), residues: 181 sheet: -2.35 (0.82), residues: 38 loop : -2.90 (0.35), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 478 TYR 0.017 0.002 TYR B 66 PHE 0.028 0.003 PHE B 321 TRP 0.026 0.003 TRP B 402 HIS 0.012 0.002 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.44 (23716) covalent geometry : angle 0.93155 / 0.45 (36170) hydrogen bonds : bond 0.10313 / 6.26 ( 636) hydrogen bonds : angle 3.59358 / 2.10 ( 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: 44 poor density : 32 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7606 (t80) REVERT: B 228 GLN cc_start: 0.8310 (pm20) cc_final: 0.7933 (pm20) REVERT: B 390 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8162 (tmm-80) REVERT: B 438 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: B 448 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8470 (tmtt) outliers start: 44 outliers final: 26 residues processed: 72 average time/residue: 0.1710 time to fit residues: 18.2561 Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 29 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 260 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 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: 4.9990 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** 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 = 0.3752 r_free = 0.3752 target = 0.095534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068273 restraints weight = 84272.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070243 restraints weight = 36138.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.071461 restraints weight = 24114.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072067 restraints weight = 19717.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.072362 restraints weight = 17866.210| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23716 Z= 0.153 Angle : 0.620 13.758 36170 Z= 0.310 Chirality : 0.032 0.362 4687 Planarity : 0.005 0.089 1481 Dihedral : 25.357 171.145 12843 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.66 % Allowed : 14.25 % Favored : 85.09 % Rotamer: Outliers : 7.65 % Allowed : 35.97 % Favored : 56.38 % 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: -3.17 (0.37), residues: 456 helix: -1.71 (0.37), residues: 189 sheet: -1.64 (1.09), residues: 22 loop : -2.52 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 301 TYR 0.016 0.001 TYR B 66 PHE 0.017 0.001 PHE B 321 TRP 0.021 0.002 TRP B 471 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (23716) covalent geometry : angle 0.61960 / 0.31 (36170) hydrogen bonds : bond 0.06886 / 4.09 ( 636) hydrogen bonds : angle 2.82572 / 1.62 ( 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 69 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8205 (OUTLIER) cc_final: 0.7480 (m-90) REVERT: B 66 TYR cc_start: 0.7931 (t80) cc_final: 0.7445 (t80) REVERT: B 226 TRP cc_start: 0.7385 (t60) cc_final: 0.6963 (t60) REVERT: B 228 GLN cc_start: 0.8043 (pm20) cc_final: 0.7632 (pm20) REVERT: B 328 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7897 (mtmm) REVERT: B 390 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7662 (tmm-80) outliers start: 30 outliers final: 18 residues processed: 64 average time/residue: 0.1624 time to fit residues: 15.9132 Evaluate side-chains 58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 37 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP 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 178 VAL Chi-restraints excluded: chain B residue 224 PHE 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 328 LYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 355 GLU 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 458 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 119 optimal weight: 0.2980 chunk 81 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 59 optimal weight: 7.9990 chunk 117 optimal weight: 0.0770 chunk 40 optimal weight: 10.0000 overall best weight: 2.0940 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.095600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068451 restraints weight = 84927.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070285 restraints weight = 37086.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071446 restraints weight = 24750.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072070 restraints weight = 20342.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072350 restraints weight = 18467.980| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23716 Z= 0.172 Angle : 0.616 14.109 36170 Z= 0.309 Chirality : 0.032 0.363 4687 Planarity : 0.005 0.090 1481 Dihedral : 25.341 171.598 12843 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.01 % Favored : 83.33 % Rotamer: Outliers : 7.14 % Allowed : 37.24 % 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: -2.97 (0.37), residues: 456 helix: -1.58 (0.37), residues: 188 sheet: -1.46 (1.09), residues: 22 loop : -2.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 401 TYR 0.017 0.001 TYR B 66 PHE 0.010 0.001 PHE B 321 TRP 0.013 0.001 TRP B 226 HIS 0.004 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (23716) covalent geometry : angle 0.61637 / 0.31 (36170) hydrogen bonds : bond 0.06778 / 4.03 ( 636) hydrogen bonds : angle 2.81120 / 1.60 ( 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 66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 38 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.7410 (m-90) REVERT: B 74 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8170 (mtm-85) REVERT: B 226 TRP cc_start: 0.7270 (t60) cc_final: 0.6723 (t60) REVERT: B 228 GLN cc_start: 0.7912 (pm20) cc_final: 0.7570 (pm20) REVERT: B 328 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7955 (mtmm) REVERT: B 390 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7521 (tmm-80) outliers start: 28 outliers final: 19 residues processed: 61 average time/residue: 0.1742 time to fit residues: 16.0252 Evaluate side-chains 58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 35 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 129 LEU 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 270 LEU Chi-restraints excluded: chain B residue 278 VAL 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 328 LYS Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 349 ILE 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 458 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 113 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 67 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 118 optimal weight: 0.0670 chunk 23 optimal weight: 7.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS ** 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 = 0.095079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068020 restraints weight = 85304.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069714 restraints weight = 37335.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070837 restraints weight = 25008.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071459 restraints weight = 20580.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071810 restraints weight = 18660.826| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23716 Z= 0.225 Angle : 0.648 14.441 36170 Z= 0.322 Chirality : 0.034 0.365 4687 Planarity : 0.005 0.092 1481 Dihedral : 25.332 171.744 12843 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.79 % Favored : 83.55 % Rotamer: Outliers : 7.65 % Allowed : 36.22 % 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: -2.94 (0.37), residues: 456 helix: -1.53 (0.37), residues: 188 sheet: -1.62 (1.09), residues: 23 loop : -2.36 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 401 TYR 0.018 0.001 TYR B 66 PHE 0.010 0.002 PHE B 321 TRP 0.020 0.002 TRP B 59 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (23716) covalent geometry : angle 0.64786 / 0.32 (36170) hydrogen bonds : bond 0.06979 / 4.15 ( 636) hydrogen bonds : angle 2.87366 / 1.65 ( 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 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7432 (m-90) REVERT: B 74 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8244 (mtm-85) REVERT: B 228 GLN cc_start: 0.8126 (pm20) cc_final: 0.7787 (pm20) REVERT: B 328 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7982 (mtmm) REVERT: B 390 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7517 (tmm-80) outliers start: 30 outliers final: 23 residues processed: 59 average time/residue: 0.1878 time to fit residues: 16.4989 Evaluate side-chains 61 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 34 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP 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 148 GLU 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 270 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 279 VAL 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 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 458 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.094956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067757 restraints weight = 85181.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069572 restraints weight = 37312.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070726 restraints weight = 24961.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071350 restraints weight = 20519.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071640 restraints weight = 18637.023| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23716 Z= 0.221 Angle : 0.646 14.188 36170 Z= 0.321 Chirality : 0.033 0.364 4687 Planarity : 0.005 0.092 1481 Dihedral : 25.348 171.666 12843 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.66 % Allowed : 16.01 % Favored : 83.33 % Rotamer: Outliers : 7.40 % Allowed : 35.46 % Favored : 57.14 % 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: -2.90 (0.37), residues: 456 helix: -1.49 (0.38), residues: 188 sheet: -1.33 (1.10), residues: 22 loop : -2.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 401 TYR 0.013 0.001 TYR B 66 PHE 0.009 0.002 PHE B 430 TRP 0.021 0.002 TRP B 226 HIS 0.006 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (23716) covalent geometry : angle 0.64612 / 0.32 (36170) hydrogen bonds : bond 0.07023 / 4.18 ( 636) hydrogen bonds : angle 2.86633 / 1.65 ( 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 64 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 35 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8202 (OUTLIER) cc_final: 0.7428 (m-90) REVERT: B 74 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8230 (mtm-85) REVERT: B 228 GLN cc_start: 0.8085 (pm20) cc_final: 0.7718 (pm20) REVERT: B 328 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7996 (mtmm) REVERT: B 390 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7511 (tmm-80) REVERT: B 448 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8479 (tmtt) outliers start: 29 outliers final: 22 residues processed: 59 average time/residue: 0.1726 time to fit residues: 15.1204 Evaluate side-chains 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 33 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP 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 148 GLU Chi-restraints excluded: chain B residue 168 THR 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 328 LYS 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 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 448 LYS Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 88 optimal weight: 0.0270 overall best weight: 3.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.094819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.067751 restraints weight = 84891.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069460 restraints weight = 37320.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070565 restraints weight = 25003.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071194 restraints weight = 20611.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071479 restraints weight = 18720.643| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23716 Z= 0.237 Angle : 0.656 14.289 36170 Z= 0.325 Chirality : 0.034 0.366 4687 Planarity : 0.005 0.093 1481 Dihedral : 25.346 171.780 12843 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.79 % Favored : 83.55 % Rotamer: Outliers : 8.42 % Allowed : 34.69 % Favored : 56.89 % 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: -2.91 (0.37), residues: 456 helix: -1.50 (0.37), residues: 188 sheet: -1.32 (1.10), residues: 22 loop : -2.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 401 TYR 0.015 0.001 TYR B 66 PHE 0.010 0.002 PHE B 430 TRP 0.017 0.002 TRP B 226 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (23716) covalent geometry : angle 0.65563 / 0.33 (36170) hydrogen bonds : bond 0.07082 / 4.22 ( 636) hydrogen bonds : angle 2.88738 / 1.66 ( 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 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 32 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8195 (OUTLIER) cc_final: 0.7424 (m-90) REVERT: B 74 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8234 (mtm-85) REVERT: B 228 GLN cc_start: 0.8094 (pm20) cc_final: 0.7736 (pm20) REVERT: B 328 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8002 (mtmm) REVERT: B 390 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7518 (tmm-80) REVERT: B 448 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8481 (tmtt) REVERT: B 453 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7961 (mmt180) outliers start: 33 outliers final: 25 residues processed: 62 average time/residue: 0.1754 time to fit residues: 16.1655 Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP 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 116 ARG Chi-restraints excluded: chain B residue 129 LEU 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 178 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 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 350 ARG 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 448 LYS Chi-restraints excluded: chain B residue 453 ARG 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: 2.9990 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.096264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.069066 restraints weight = 85232.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071035 restraints weight = 36797.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072241 restraints weight = 24633.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072878 restraints weight = 20213.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073180 restraints weight = 18291.995| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23716 Z= 0.153 Angle : 0.598 14.657 36170 Z= 0.298 Chirality : 0.031 0.369 4687 Planarity : 0.005 0.093 1481 Dihedral : 25.264 174.661 12843 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.66 % Allowed : 15.13 % Favored : 84.21 % Rotamer: Outliers : 7.91 % Allowed : 35.20 % Favored : 56.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.32 (0.38), residues: 189 sheet: -1.33 (1.08), residues: 22 loop : -2.31 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 401 TYR 0.017 0.001 TYR B 66 PHE 0.009 0.001 PHE B 321 TRP 0.020 0.001 TRP B 226 HIS 0.005 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (23716) covalent geometry : angle 0.59763 / 0.30 (36170) hydrogen bonds : bond 0.06560 / 3.90 ( 636) hydrogen bonds : angle 2.70995 / 1.54 ( 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 66 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 35 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: B 74 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8236 (mtm-85) REVERT: B 228 GLN cc_start: 0.8033 (pm20) cc_final: 0.7697 (pm20) REVERT: B 328 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8003 (mtmm) REVERT: B 390 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7504 (tmm-80) REVERT: B 448 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8449 (tmtt) REVERT: B 453 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7910 (mmt180) outliers start: 31 outliers final: 22 residues processed: 61 average time/residue: 0.1673 time to fit residues: 15.2901 Evaluate side-chains 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 TRP 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 148 GLU Chi-restraints excluded: chain B residue 168 THR 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 350 ARG 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 448 LYS Chi-restraints excluded: chain B residue 453 ARG 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 32 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 HIS ** 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 = 0.3737 r_free = 0.3737 target = 0.094457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067031 restraints weight = 85870.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.068876 restraints weight = 38295.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070011 restraints weight = 26053.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070647 restraints weight = 21575.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070802 restraints weight = 19590.114| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23716 Z= 0.278 Angle : 0.700 13.914 36170 Z= 0.342 Chirality : 0.034 0.374 4687 Planarity : 0.006 0.094 1481 Dihedral : 25.320 173.929 12843 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.66 % Allowed : 17.32 % Favored : 82.02 % Rotamer: Outliers : 7.40 % Allowed : 35.46 % Favored : 57.14 % 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: -2.88 (0.38), residues: 456 helix: -1.45 (0.37), residues: 188 sheet: -1.45 (1.11), residues: 23 loop : -2.38 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 401 TYR 0.013 0.002 TYR B 66 PHE 0.011 0.002 PHE B 430 TRP 0.018 0.002 TRP B 402 HIS 0.010 0.002 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.28 (23716) covalent geometry : angle 0.70028 / 0.34 (36170) hydrogen bonds : bond 0.07528 / 4.48 ( 636) hydrogen bonds : angle 2.98365 / 1.71 ( 1187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.86 seconds wall clock time: 67 minutes 37.48 seconds (4057.48 seconds total)