Starting phenix.real_space_refine on Tue Aug 4 16:45:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.cif Found real_map, /net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.map" model { file = "/net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28wy_56930/08_2026/28wy_56930.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3121 2.51 5 N 890 2.21 5 O 901 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4929 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1883 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 277} Chain breaks: 5 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 578 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 16, 'ARG:plan': 22, 'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 282 Chain: "B" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2649 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain breaks: 2 Unresolved non-hydrogen bonds: 453 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 383 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 10, 'TYR:plan': 6, 'GLU:plan': 12, 'ASP:plan': 9, 'ARG:plan': 6, 'PHE:plan': 7, 'HIS:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 287 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain breaks: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.27 Number of scatterers: 4929 At special positions: 0 Unit cell: (58.37, 105.066, 108.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 901 8.00 N 890 7.00 C 3121 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: 0.42 Conformation dependent library (CDL) restraints added in 232.8 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 76.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 141 through 160 Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'A' and resid 197 through 218 Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 239 through 248 removed outlier: 3.662A pdb=" N GLN A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.535A pdb=" N THR A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 312 removed outlier: 4.347A pdb=" N CYS A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N HIS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 332 through 344 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 55 through 75 Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 103 through 128 removed outlier: 4.288A pdb=" N VAL B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 164 through 182 removed outlier: 4.486A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.250A pdb=" N CYS B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 225 through 240 Processing helix chain 'B' and resid 244 through 263 removed outlier: 3.588A pdb=" N TYR B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.743A pdb=" N LEU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 removed outlier: 3.779A pdb=" N ALA B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 334 removed outlier: 3.656A pdb=" N ILE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 394 through 399 removed outlier: 4.076A pdb=" N VAL B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.811A pdb=" N ALA C 36 " --> pdb=" O ASP C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 64 removed outlier: 3.661A pdb=" N HIS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 320 removed outlier: 3.724A pdb=" N GLN A 317 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 removed outlier: 4.289A pdb=" N MET B 265 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 375 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.57 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: 1176 1.33 - 1.46: 987 1.46 - 1.58: 2826 1.58 - 1.70: 1 1.70 - 1.83: 25 Bond restraints: 5015 Sorted by residual: bond pdb=" N PRO B 56 " pdb=" CA PRO B 56 " ideal model delta sigma weight residual 1.465 1.522 -0.057 2.03e-02 2.43e+03 7.81e+00 bond pdb=" C ASN B 390 " pdb=" N PRO B 391 " ideal model delta sigma weight residual 1.335 1.364 -0.030 1.28e-02 6.10e+03 5.45e+00 bond pdb=" C PRO A 257 " pdb=" N PRO A 258 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.30e-02 5.92e+03 5.39e+00 bond pdb=" CB ARG B 323 " pdb=" CG ARG B 323 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.05e+00 bond pdb=" N PRO A 257 " pdb=" CA PRO A 257 " ideal model delta sigma weight residual 1.465 1.509 -0.044 2.03e-02 2.43e+03 4.75e+00 ... (remaining 5010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 6596 2.88 - 5.76: 223 5.76 - 8.65: 27 8.65 - 11.53: 3 11.53 - 14.41: 1 Bond angle restraints: 6850 Sorted by residual: angle pdb=" N PRO B 56 " pdb=" CA PRO B 56 " pdb=" C PRO B 56 " ideal model delta sigma weight residual 110.70 118.41 -7.71 1.22e+00 6.72e-01 4.00e+01 angle pdb=" N PRO A 257 " pdb=" CA PRO A 257 " pdb=" C PRO A 257 " ideal model delta sigma weight residual 110.70 116.84 -6.14 1.22e+00 6.72e-01 2.54e+01 angle pdb=" CG1 ILE B 310 " pdb=" CB ILE B 310 " pdb=" CG2 ILE B 310 " ideal model delta sigma weight residual 110.70 96.29 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N ASP C 35 " pdb=" CA ASP C 35 " pdb=" C ASP C 35 " ideal model delta sigma weight residual 111.71 116.50 -4.79 1.15e+00 7.56e-01 1.74e+01 angle pdb=" CA PRO B 56 " pdb=" C PRO B 56 " pdb=" N PRO B 57 " ideal model delta sigma weight residual 117.93 122.87 -4.94 1.20e+00 6.94e-01 1.69e+01 ... (remaining 6845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 2808 16.07 - 32.14: 167 32.14 - 48.21: 27 48.21 - 64.29: 10 64.29 - 80.36: 4 Dihedral angle restraints: 3016 sinusoidal: 894 harmonic: 2122 Sorted by residual: dihedral pdb=" CA ASP B 162 " pdb=" C ASP B 162 " pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA HIS C 37 " pdb=" C HIS C 37 " pdb=" N VAL C 38 " pdb=" CA VAL C 38 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL B 29 " pdb=" C VAL B 29 " pdb=" N SER B 30 " pdb=" CA SER B 30 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 3013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 684 0.076 - 0.152: 103 0.152 - 0.228: 22 0.228 - 0.304: 2 0.304 - 0.380: 1 Chirality restraints: 812 Sorted by residual: chirality pdb=" CB ILE B 310 " pdb=" CA ILE B 310 " pdb=" CG1 ILE B 310 " pdb=" CG2 ILE B 310 " both_signs ideal model delta sigma weight residual False 2.64 3.02 -0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA HIS B 239 " pdb=" N HIS B 239 " pdb=" C HIS B 239 " pdb=" CB HIS B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU B 256 " pdb=" N LEU B 256 " pdb=" C LEU B 256 " pdb=" CB LEU B 256 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 809 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 390 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ASN B 390 " 0.058 2.00e-02 2.50e+03 pdb=" O ASN B 390 " -0.022 2.00e-02 2.50e+03 pdb=" N PRO B 391 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 392 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PHE B 392 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE B 392 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO B 393 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 222 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C HIS A 222 " 0.055 2.00e-02 2.50e+03 pdb=" O HIS A 222 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 223 " -0.018 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 2731 3.07 - 3.53: 5206 3.53 - 3.98: 7743 3.98 - 4.44: 8710 4.44 - 4.90: 12803 Nonbonded interactions: 37193 Sorted by model distance: nonbonded pdb=" N THR A 313 " pdb=" O THR A 313 " model vdw 2.609 2.496 nonbonded pdb=" N ASP A 59 " pdb=" O ASP A 59 " model vdw 2.632 2.496 nonbonded pdb=" N LYS A 315 " pdb=" O LYS A 315 " model vdw 2.638 2.496 nonbonded pdb=" N GLU C 25 " pdb=" O GLU C 25 " model vdw 2.644 2.496 nonbonded pdb=" N LEU A 356 " pdb=" O LEU A 356 " model vdw 2.647 2.496 ... (remaining 37188 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.740 Find NCS groups from input model: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 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 : 0.007 0.072 5015 Z= 0.349 Angle : 1.248 14.411 6850 Z= 0.794 Chirality : 0.061 0.380 812 Planarity : 0.010 0.105 916 Dihedral : 12.049 80.357 1624 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 0.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.26 (0.29), residues: 704 helix: 0.49 (0.20), residues: 514 sheet: -1.29 (1.12), residues: 20 loop : -0.26 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG A 276 TYR 0.032 0.006 TYR B 376 PHE 0.031 0.003 PHE A 228 TRP 0.031 0.005 TRP C 27 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.35 ( 5015) covalent geometry : angle 1.24829 / 0.79 ( 6850) hydrogen bonds : bond 0.20494 / 15.01 ( 375) hydrogen bonds : angle 6.71495 / 4.93 ( 1101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 THR cc_start: 0.8384 (m) cc_final: 0.7910 (m) REVERT: B 378 SER cc_start: 0.7430 (t) cc_final: 0.6601 (p) REVERT: C 34 GLU cc_start: 0.7546 (tt0) cc_final: 0.6951 (tt0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0694 time to fit residues: 13.9262 Evaluate side-chains 81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS B 247 ASN B 275 HIS B 372 HIS C 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.120774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103448 restraints weight = 15879.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.105996 restraints weight = 9065.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107754 restraints weight = 6110.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.108957 restraints weight = 4596.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109716 restraints weight = 3702.989| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5015 Z= 0.158 Angle : 0.627 6.473 6850 Z= 0.347 Chirality : 0.040 0.168 812 Planarity : 0.005 0.034 916 Dihedral : 4.738 22.667 754 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.21 % Allowed : 13.64 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.50 (0.32), residues: 704 helix: 2.00 (0.22), residues: 518 sheet: -0.46 (1.95), residues: 10 loop : 0.93 (0.53), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 323 TYR 0.034 0.002 TYR A 215 PHE 0.027 0.002 PHE B 170 TRP 0.018 0.002 TRP C 27 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 5015) covalent geometry : angle 0.62724 / 0.35 ( 6850) hydrogen bonds : bond 0.04843 / 3.52 ( 375) hydrogen bonds : angle 4.46101 / 3.24 ( 1101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6663 (pt0) REVERT: A 215 TYR cc_start: 0.6448 (m-80) cc_final: 0.5898 (m-80) REVERT: B 378 SER cc_start: 0.7007 (t) cc_final: 0.6610 (p) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 0.0644 time to fit residues: 8.4439 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 370 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.117811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.100286 restraints weight = 16090.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.102726 restraints weight = 9205.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.104386 restraints weight = 6252.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.105512 restraints weight = 4737.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106200 restraints weight = 3870.855| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5015 Z= 0.198 Angle : 0.624 6.420 6850 Z= 0.332 Chirality : 0.040 0.175 812 Planarity : 0.005 0.045 916 Dihedral : 4.543 19.576 754 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.01 % Allowed : 14.71 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.50 (0.32), residues: 704 helix: 2.03 (0.22), residues: 517 sheet: -0.84 (2.06), residues: 10 loop : 0.88 (0.53), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.027 0.002 TYR A 215 PHE 0.023 0.002 PHE B 170 TRP 0.010 0.002 TRP C 27 HIS 0.009 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 5015) covalent geometry : angle 0.62380 / 0.33 ( 6850) hydrogen bonds : bond 0.04406 / 3.20 ( 375) hydrogen bonds : angle 4.44476 / 3.26 ( 1101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6741 (m-80) cc_final: 0.6356 (m-80) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.0683 time to fit residues: 8.6275 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 370 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN A 236 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.116533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.098191 restraints weight = 15833.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.100650 restraints weight = 9024.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.102359 restraints weight = 6095.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.103502 restraints weight = 4594.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.104237 restraints weight = 3748.074| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5015 Z= 0.148 Angle : 0.578 7.563 6850 Z= 0.303 Chirality : 0.039 0.192 812 Planarity : 0.005 0.043 916 Dihedral : 4.269 19.572 754 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.94 % Allowed : 16.84 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.55 (0.32), residues: 704 helix: 2.07 (0.23), residues: 517 sheet: -1.20 (1.93), residues: 10 loop : 0.89 (0.52), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 270 TYR 0.026 0.002 TYR A 215 PHE 0.021 0.002 PHE B 170 TRP 0.010 0.002 TRP C 39 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 5015) covalent geometry : angle 0.57816 / 0.30 ( 6850) hydrogen bonds : bond 0.03927 / 2.83 ( 375) hydrogen bonds : angle 4.18423 / 3.07 ( 1101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7070 (m-80) cc_final: 0.6750 (m-80) REVERT: B 353 GLU cc_start: 0.7959 (pm20) cc_final: 0.7735 (pm20) outliers start: 11 outliers final: 9 residues processed: 89 average time/residue: 0.0462 time to fit residues: 5.7190 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.0570 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.117655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099200 restraints weight = 16014.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.101742 restraints weight = 9056.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.103500 restraints weight = 6099.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.104696 restraints weight = 4575.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.105558 restraints weight = 3701.865| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5015 Z= 0.124 Angle : 0.565 8.777 6850 Z= 0.292 Chirality : 0.038 0.204 812 Planarity : 0.004 0.044 916 Dihedral : 4.046 19.389 754 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.67 % Allowed : 17.65 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.55 (0.32), residues: 704 helix: 2.10 (0.23), residues: 518 sheet: -1.48 (1.81), residues: 10 loop : 0.82 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 213 TYR 0.019 0.002 TYR A 215 PHE 0.018 0.001 PHE B 170 TRP 0.013 0.002 TRP C 27 HIS 0.009 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 5015) covalent geometry : angle 0.56480 / 0.29 ( 6850) hydrogen bonds : bond 0.03529 / 2.54 ( 375) hydrogen bonds : angle 4.02924 / 2.94 ( 1101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7051 (m-80) cc_final: 0.6368 (m-80) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.0368 time to fit residues: 4.7288 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 341 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS B 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.117738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.100162 restraints weight = 16152.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.102599 restraints weight = 9372.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104097 restraints weight = 6401.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105327 restraints weight = 4915.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106048 restraints weight = 4005.449| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5015 Z= 0.140 Angle : 0.577 7.906 6850 Z= 0.298 Chirality : 0.039 0.210 812 Planarity : 0.004 0.045 916 Dihedral : 4.003 19.704 754 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.67 % Allowed : 18.18 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.53 (0.32), residues: 704 helix: 2.11 (0.23), residues: 518 sheet: -1.64 (1.72), residues: 10 loop : 0.71 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.027 0.002 TYR A 215 PHE 0.014 0.002 PHE B 170 TRP 0.019 0.002 TRP C 27 HIS 0.007 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5015) covalent geometry : angle 0.57701 / 0.30 ( 6850) hydrogen bonds : bond 0.03588 / 2.58 ( 375) hydrogen bonds : angle 4.03621 / 2.95 ( 1101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7017 (m-80) cc_final: 0.6634 (m-80) outliers start: 10 outliers final: 7 residues processed: 87 average time/residue: 0.0487 time to fit residues: 5.9296 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS B 336 HIS ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.099886 restraints weight = 15982.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.102327 restraints weight = 9299.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.103941 restraints weight = 6347.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.104931 restraints weight = 4810.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.105794 restraints weight = 3985.185| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5015 Z= 0.141 Angle : 0.591 8.176 6850 Z= 0.303 Chirality : 0.039 0.211 812 Planarity : 0.005 0.044 916 Dihedral : 3.997 19.598 754 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.94 % Allowed : 19.79 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.50 (0.32), residues: 704 helix: 2.07 (0.23), residues: 520 sheet: -1.80 (1.69), residues: 10 loop : 0.75 (0.50), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.020 0.002 TYR A 215 PHE 0.013 0.002 PHE A 228 TRP 0.017 0.002 TRP C 27 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5015) covalent geometry : angle 0.59075 / 0.30 ( 6850) hydrogen bonds : bond 0.03580 / 2.58 ( 375) hydrogen bonds : angle 4.07325 / 2.97 ( 1101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7088 (m-80) cc_final: 0.6716 (m-80) REVERT: B 353 GLU cc_start: 0.7962 (pm20) cc_final: 0.7755 (pm20) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.0498 time to fit residues: 5.8946 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 275 HIS ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.117329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.099698 restraints weight = 16403.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.102118 restraints weight = 9534.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.103751 restraints weight = 6542.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104859 restraints weight = 4976.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.105578 restraints weight = 4083.284| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5015 Z= 0.141 Angle : 0.622 9.907 6850 Z= 0.320 Chirality : 0.040 0.197 812 Planarity : 0.005 0.045 916 Dihedral : 4.040 19.923 754 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.41 % Allowed : 21.12 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.39 (0.32), residues: 704 helix: 1.99 (0.23), residues: 519 sheet: -2.17 (1.63), residues: 10 loop : 0.78 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 213 TYR 0.018 0.002 TYR A 215 PHE 0.017 0.001 PHE A 232 TRP 0.017 0.002 TRP C 27 HIS 0.003 0.001 HIS B 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5015) covalent geometry : angle 0.62196 / 0.32 ( 6850) hydrogen bonds : bond 0.03532 / 2.55 ( 375) hydrogen bonds : angle 4.18057 / 3.06 ( 1101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7108 (m-80) cc_final: 0.6660 (m-80) REVERT: B 265 MET cc_start: 0.7727 (tpt) cc_final: 0.7170 (tpp) outliers start: 9 outliers final: 9 residues processed: 90 average time/residue: 0.0505 time to fit residues: 6.2555 Evaluate side-chains 85 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 275 HIS ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.115786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098026 restraints weight = 15991.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.100484 restraints weight = 8984.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.102159 restraints weight = 6007.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.103314 restraints weight = 4502.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.104038 restraints weight = 3635.898| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5015 Z= 0.144 Angle : 0.634 9.864 6850 Z= 0.327 Chirality : 0.040 0.235 812 Planarity : 0.005 0.044 916 Dihedral : 4.050 20.056 754 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.41 % Allowed : 21.39 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.43 (0.32), residues: 704 helix: 2.01 (0.23), residues: 517 sheet: -2.48 (1.60), residues: 10 loop : 0.85 (0.51), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 213 TYR 0.018 0.002 TYR A 215 PHE 0.029 0.002 PHE B 170 TRP 0.015 0.002 TRP C 27 HIS 0.007 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5015) covalent geometry : angle 0.63398 / 0.33 ( 6850) hydrogen bonds : bond 0.03499 / 2.53 ( 375) hydrogen bonds : angle 4.16437 / 3.05 ( 1101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7277 (m-80) cc_final: 0.6818 (m-80) REVERT: B 265 MET cc_start: 0.7821 (tpt) cc_final: 0.7286 (tpp) outliers start: 9 outliers final: 9 residues processed: 81 average time/residue: 0.0576 time to fit residues: 6.3450 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 275 HIS ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.117070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.099780 restraints weight = 16313.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.102149 restraints weight = 9517.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.103747 restraints weight = 6556.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.104815 restraints weight = 5007.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.105624 restraints weight = 4105.472| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5015 Z= 0.148 Angle : 0.652 10.361 6850 Z= 0.330 Chirality : 0.040 0.237 812 Planarity : 0.005 0.044 916 Dihedral : 4.059 20.164 754 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 21.66 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.40 (0.32), residues: 704 helix: 1.99 (0.23), residues: 517 sheet: -2.62 (1.61), residues: 10 loop : 0.86 (0.51), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 213 TYR 0.021 0.002 TYR A 215 PHE 0.021 0.002 PHE B 170 TRP 0.015 0.002 TRP C 27 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5015) covalent geometry : angle 0.65193 / 0.33 ( 6850) hydrogen bonds : bond 0.03481 / 2.52 ( 375) hydrogen bonds : angle 4.19585 / 3.07 ( 1101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.7127 (m-80) cc_final: 0.6670 (m-80) REVERT: B 265 MET cc_start: 0.7615 (tpt) cc_final: 0.7214 (tpp) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.0555 time to fit residues: 6.3280 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 275 HIS Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 40 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 0.0000 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 275 HIS ** B 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.117045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099862 restraints weight = 16055.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.102213 restraints weight = 9364.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.103873 restraints weight = 6445.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.104811 restraints weight = 4879.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.105729 restraints weight = 4066.274| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5015 Z= 0.144 Angle : 0.664 10.843 6850 Z= 0.331 Chirality : 0.040 0.228 812 Planarity : 0.004 0.044 916 Dihedral : 4.046 20.221 754 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.67 % Allowed : 22.19 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 2.40 (0.33), residues: 704 helix: 1.99 (0.23), residues: 517 sheet: -3.03 (1.39), residues: 12 loop : 0.89 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 213 TYR 0.018 0.002 TYR A 215 PHE 0.019 0.002 PHE B 170 TRP 0.016 0.002 TRP C 27 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5015) covalent geometry : angle 0.66382 / 0.33 ( 6850) hydrogen bonds : bond 0.03450 / 2.49 ( 375) hydrogen bonds : angle 4.19172 / 3.07 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 922.64 seconds wall clock time: 16 minutes 33.15 seconds (993.15 seconds total)