Starting phenix.real_space_refine on Wed Mar 4 06:06:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryp_24744/03_2026/7ryp_24744.cif" } resolution = 4.8 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= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 3598 2.51 5 N 992 2.21 5 O 1074 1.98 5 H 5599 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11293 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 4877 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 324} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 6416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6416 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 8, 'TRANS': 383} Chain breaks: 5 Time building chain proxies: 2.02, per 1000 atoms: 0.18 Number of scatterers: 11293 At special positions: 0 Unit cell: (70.56, 103.88, 117.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1074 8.00 N 992 7.00 C 3598 6.00 H 5599 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 313.5 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 61.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 89 through 100 removed outlier: 3.573A pdb=" N ILE A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 134 through 154 Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 275 through 291 Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'B' and resid 6 through 22 Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.568A pdb=" N GLU B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.626A pdb=" N LEU B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 Processing helix chain 'B' and resid 201 through 222 removed outlier: 4.031A pdb=" N THR B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'B' and resid 245 through 263 removed outlier: 3.610A pdb=" N GLN B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 removed outlier: 5.063A pdb=" N HIS B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 326 removed outlier: 6.224A pdb=" N LYS B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 328 No H-bonds generated for 'chain 'B' and resid 327 through 328' Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 346 through 361 removed outlier: 4.473A pdb=" N ARG B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.818A pdb=" N GLU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 410 removed outlier: 4.050A pdb=" N VAL B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 440 through 455 Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 464 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 7.300A pdb=" N VAL A 29 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N ALA A 76 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 31 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS A 28 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ALA A 338 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 30 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL A 340 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG A 32 " --> pdb=" O VAL A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.866A pdb=" N GLY A 103 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 264 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 105 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 160 removed outlier: 4.116A pdb=" N CYS A 162 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 187 348 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5584 1.13 - 1.30: 962 1.30 - 1.47: 2320 1.47 - 1.64: 2483 1.64 - 1.81: 45 Bond restraints: 11394 Sorted by residual: bond pdb=" CD1 TYR B 128 " pdb=" HD1 TYR B 128 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" CD2 TYR B 128 " pdb=" HD2 TYR B 128 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CE1 TYR B 128 " pdb=" HE1 TYR B 128 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" CD2 PHE B 13 " pdb=" HD2 PHE B 13 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" CE2 TYR B 128 " pdb=" HE2 TYR B 128 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.55e+01 ... (remaining 11389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 18277 2.72 - 5.43: 1690 5.43 - 8.15: 477 8.15 - 10.87: 13 10.87 - 13.58: 16 Bond angle restraints: 20473 Sorted by residual: angle pdb=" C HIS A 341 " pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 119.84 131.10 -11.26 1.25e+00 6.40e-01 8.12e+01 angle pdb=" C GLY B 51 " pdb=" N PRO B 52 " pdb=" CA PRO B 52 " ideal model delta sigma weight residual 119.47 129.82 -10.35 1.16e+00 7.43e-01 7.96e+01 angle pdb=" C ARG B 385 " pdb=" N PRO B 386 " pdb=" CA PRO B 386 " ideal model delta sigma weight residual 120.03 128.56 -8.53 9.90e-01 1.02e+00 7.43e+01 angle pdb=" C HIS B 245 " pdb=" N PRO B 246 " pdb=" CA PRO B 246 " ideal model delta sigma weight residual 119.32 128.24 -8.92 1.14e+00 7.69e-01 6.12e+01 angle pdb=" C GLU A 66 " pdb=" N PRO A 67 " pdb=" CA PRO A 67 " ideal model delta sigma weight residual 119.76 127.78 -8.02 1.03e+00 9.43e-01 6.06e+01 ... (remaining 20468 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 5066 16.68 - 33.36: 169 33.36 - 50.05: 63 50.05 - 66.73: 35 66.73 - 83.41: 6 Dihedral angle restraints: 5339 sinusoidal: 2841 harmonic: 2498 Sorted by residual: dihedral pdb=" CA ALA B 53 " pdb=" C ALA B 53 " pdb=" N PRO B 54 " pdb=" CA PRO B 54 " ideal model delta harmonic sigma weight residual 180.00 138.23 41.77 0 5.00e+00 4.00e-02 6.98e+01 dihedral pdb=" CD2 HIS B 419 " pdb=" CG HIS B 419 " pdb=" ND1 HIS B 419 " pdb=" HD1 HIS B 419 " ideal model delta harmonic sigma weight residual 180.00 -144.98 -35.02 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CD2 HIS A 237 " pdb=" CG HIS A 237 " pdb=" ND1 HIS A 237 " pdb=" HD1 HIS A 237 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 427 0.048 - 0.096: 287 0.096 - 0.145: 117 0.145 - 0.193: 34 0.193 - 0.241: 6 Chirality restraints: 871 Sorted by residual: chirality pdb=" CA TYR B 466 " pdb=" N TYR B 466 " pdb=" C TYR B 466 " pdb=" CB TYR B 466 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA SER B 357 " pdb=" N SER B 357 " pdb=" C SER B 357 " pdb=" CB SER B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 133 " pdb=" N ARG A 133 " pdb=" C ARG A 133 " pdb=" CB ARG A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 868 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 419 " 0.130 2.00e-02 2.50e+03 1.31e-01 3.87e+02 pdb=" CG HIS B 419 " 0.060 2.00e-02 2.50e+03 pdb=" ND1 HIS B 419 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS B 419 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 HIS B 419 " 0.069 2.00e-02 2.50e+03 pdb=" NE2 HIS B 419 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 HIS B 419 " -0.306 2.00e-02 2.50e+03 pdb=" HD2 HIS B 419 " -0.100 2.00e-02 2.50e+03 pdb=" HE1 HIS B 419 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 237 " -0.091 2.00e-02 2.50e+03 9.23e-02 1.92e+02 pdb=" CG HIS A 237 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS A 237 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS A 237 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 237 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 HIS A 237 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 HIS A 237 " 0.214 2.00e-02 2.50e+03 pdb=" HD2 HIS A 237 " 0.072 2.00e-02 2.50e+03 pdb=" HE1 HIS A 237 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 479 " 0.074 2.00e-02 2.50e+03 6.97e-02 1.09e+02 pdb=" CG HIS B 479 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 479 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS B 479 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS B 479 " 0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS B 479 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 HIS B 479 " -0.161 2.00e-02 2.50e+03 pdb=" HD2 HIS B 479 " -0.056 2.00e-02 2.50e+03 pdb=" HE1 HIS B 479 " 0.055 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.90: 210 1.90 - 2.57: 11895 2.57 - 3.25: 35013 3.25 - 3.92: 42067 3.92 - 4.60: 64429 Nonbonded interactions: 153614 Sorted by model distance: nonbonded pdb=" OE1 GLU B 309 " pdb=" H GLU B 309 " model vdw 1.222 2.450 nonbonded pdb=" OE1 GLU B 225 " pdb=" H GLU B 225 " model vdw 1.265 2.450 nonbonded pdb=" OE1 GLU B 248 " pdb=" H GLU B 248 " model vdw 1.306 2.450 nonbonded pdb=" OE1 GLU B 204 " pdb=" H GLU B 204 " model vdw 1.335 2.450 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.342 2.450 ... (remaining 153609 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: 1.920 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: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.610 Find NCS groups from input model: 0.040 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: 0.000 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: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.015 0.070 5795 Z= 0.973 Angle : 1.503 11.263 7813 Z= 1.036 Chirality : 0.073 0.241 871 Planarity : 0.007 0.049 1007 Dihedral : 10.944 83.409 2118 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 1.70 % Allowed : 6.22 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 7.69 % 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: -1.44 (0.29), residues: 707 helix: -0.35 (0.22), residues: 413 sheet: -0.45 (0.67), residues: 58 loop : -2.02 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.053 0.007 TYR A 212 PHE 0.027 0.005 PHE B 410 TRP 0.023 0.007 TRP B 314 HIS 0.006 0.001 HIS B 419 Details of bonding type rmsd covalent geometry : bond 0.01493 ( 5795) covalent geometry : angle 1.50338 ( 7813) hydrogen bonds : bond 0.20366 ( 340) hydrogen bonds : angle 8.04569 ( 1011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9050 (t0) cc_final: 0.8658 (p0) REVERT: A 179 ASP cc_start: 0.8972 (t0) cc_final: 0.8582 (t0) REVERT: A 212 TYR cc_start: 0.9090 (p90) cc_final: 0.8629 (p90) REVERT: A 371 GLU cc_start: 0.9337 (tt0) cc_final: 0.8832 (pm20) REVERT: A 372 ASP cc_start: 0.9300 (t70) cc_final: 0.9084 (t0) REVERT: B 142 GLN cc_start: 0.9282 (tt0) cc_final: 0.8861 (tt0) REVERT: B 237 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8666 (tpp80) REVERT: B 443 ARG cc_start: 0.9649 (ttp80) cc_final: 0.9270 (mtm110) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1747 time to fit residues: 41.5614 Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.087709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069993 restraints weight = 71612.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073845 restraints weight = 39751.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076708 restraints weight = 25103.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.078743 restraints weight = 17091.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.080241 restraints weight = 12334.612| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5795 Z= 0.171 Angle : 0.677 8.378 7813 Z= 0.388 Chirality : 0.041 0.176 871 Planarity : 0.005 0.056 1007 Dihedral : 5.721 50.305 786 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.06 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.16 (0.30), residues: 707 helix: 0.19 (0.24), residues: 411 sheet: -0.81 (0.61), residues: 63 loop : -2.45 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.016 0.002 TYR B 169 PHE 0.022 0.002 PHE A 347 TRP 0.005 0.001 TRP B 6 HIS 0.006 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5795) covalent geometry : angle 0.67679 ( 7813) hydrogen bonds : bond 0.07226 ( 340) hydrogen bonds : angle 6.51528 ( 1011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 VAL cc_start: 0.8206 (t) cc_final: 0.7995 (t) REVERT: A 164 CYS cc_start: 0.9055 (m) cc_final: 0.8783 (m) REVERT: A 179 ASP cc_start: 0.8991 (t0) cc_final: 0.8629 (t0) REVERT: A 371 GLU cc_start: 0.9347 (tt0) cc_final: 0.8814 (pm20) REVERT: B 94 LEU cc_start: 0.9369 (mt) cc_final: 0.9070 (mt) REVERT: B 142 GLN cc_start: 0.9122 (tt0) cc_final: 0.8620 (tt0) REVERT: B 265 CYS cc_start: 0.9060 (t) cc_final: 0.8727 (t) REVERT: B 268 GLU cc_start: 0.8955 (tt0) cc_final: 0.8086 (tt0) REVERT: B 272 CYS cc_start: 0.9554 (m) cc_final: 0.9348 (m) REVERT: B 322 MET cc_start: 0.9681 (mmp) cc_final: 0.9282 (mmm) REVERT: B 389 PHE cc_start: 0.8619 (m-80) cc_final: 0.8365 (m-80) REVERT: B 440 MET cc_start: 0.9119 (mmt) cc_final: 0.7731 (mpp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1665 time to fit residues: 37.5801 Evaluate side-chains 144 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 324 ASN B 464 GLN B 470 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.083600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065837 restraints weight = 79531.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069510 restraints weight = 44409.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072207 restraints weight = 28472.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.074174 restraints weight = 19823.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075672 restraints weight = 14625.676| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5795 Z= 0.256 Angle : 0.705 9.101 7813 Z= 0.418 Chirality : 0.039 0.147 871 Planarity : 0.005 0.059 1007 Dihedral : 5.839 54.476 786 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.61 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.45 (0.30), residues: 707 helix: -0.06 (0.24), residues: 410 sheet: -0.73 (0.62), residues: 65 loop : -2.61 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 442 TYR 0.022 0.002 TYR B 172 PHE 0.024 0.003 PHE B 389 TRP 0.008 0.001 TRP B 249 HIS 0.011 0.002 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5795) covalent geometry : angle 0.70505 ( 7813) hydrogen bonds : bond 0.06558 ( 340) hydrogen bonds : angle 6.68220 ( 1011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9020 (t0) cc_final: 0.8426 (p0) REVERT: A 164 CYS cc_start: 0.9160 (m) cc_final: 0.8628 (p) REVERT: A 168 GLU cc_start: 0.7190 (tt0) cc_final: 0.6723 (tp30) REVERT: A 179 ASP cc_start: 0.8985 (t0) cc_final: 0.8596 (t0) REVERT: A 250 SER cc_start: 0.8494 (t) cc_final: 0.8160 (t) REVERT: B 94 LEU cc_start: 0.9481 (mt) cc_final: 0.9217 (mt) REVERT: B 142 GLN cc_start: 0.9213 (tt0) cc_final: 0.8806 (tt0) REVERT: B 258 GLN cc_start: 0.9347 (tp40) cc_final: 0.9101 (tp-100) REVERT: B 265 CYS cc_start: 0.9017 (t) cc_final: 0.8800 (t) REVERT: B 268 GLU cc_start: 0.9123 (tt0) cc_final: 0.8553 (tt0) REVERT: B 389 PHE cc_start: 0.8864 (m-80) cc_final: 0.8660 (m-80) REVERT: B 426 HIS cc_start: 0.9303 (t70) cc_final: 0.9076 (t-170) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1749 time to fit residues: 35.2527 Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064614 restraints weight = 81284.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.068065 restraints weight = 45698.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070649 restraints weight = 29505.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072554 restraints weight = 20687.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.073984 restraints weight = 15388.199| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5795 Z= 0.304 Angle : 0.752 9.019 7813 Z= 0.444 Chirality : 0.040 0.141 871 Planarity : 0.006 0.062 1007 Dihedral : 6.075 49.619 786 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.59 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.92 (0.30), residues: 707 helix: -0.39 (0.24), residues: 400 sheet: -0.38 (0.75), residues: 50 loop : -2.85 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 385 TYR 0.030 0.002 TYR B 317 PHE 0.030 0.003 PHE B 389 TRP 0.021 0.002 TRP B 314 HIS 0.011 0.002 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 5795) covalent geometry : angle 0.75209 ( 7813) hydrogen bonds : bond 0.06319 ( 340) hydrogen bonds : angle 6.87023 ( 1011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 CYS cc_start: 0.9275 (m) cc_final: 0.8667 (p) REVERT: A 168 GLU cc_start: 0.7136 (tt0) cc_final: 0.6523 (tp30) REVERT: A 179 ASP cc_start: 0.9048 (t0) cc_final: 0.8704 (t0) REVERT: A 212 TYR cc_start: 0.9189 (p90) cc_final: 0.8938 (p90) REVERT: A 371 GLU cc_start: 0.9553 (tt0) cc_final: 0.9217 (tt0) REVERT: B 94 LEU cc_start: 0.9509 (mt) cc_final: 0.9257 (mt) REVERT: B 142 GLN cc_start: 0.9222 (tt0) cc_final: 0.8791 (tt0) REVERT: B 223 MET cc_start: 0.7107 (mmt) cc_final: 0.6471 (mmm) REVERT: B 258 GLN cc_start: 0.9265 (tp40) cc_final: 0.8938 (tp-100) REVERT: B 259 PHE cc_start: 0.9649 (t80) cc_final: 0.9128 (t80) REVERT: B 268 GLU cc_start: 0.9259 (tt0) cc_final: 0.8670 (tt0) REVERT: B 306 ARG cc_start: 0.8781 (ptt180) cc_final: 0.8538 (ptt180) REVERT: B 316 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9131 (mtpt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1612 time to fit residues: 31.1870 Evaluate side-chains 119 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** 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 = 0.3516 r_free = 0.3516 target = 0.082385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065058 restraints weight = 75770.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068662 restraints weight = 42077.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071317 restraints weight = 26731.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073271 restraints weight = 18449.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.074706 restraints weight = 13525.885| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5795 Z= 0.227 Angle : 0.648 9.856 7813 Z= 0.382 Chirality : 0.039 0.140 871 Planarity : 0.005 0.063 1007 Dihedral : 5.894 49.354 786 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.02 % Favored : 87.69 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.77 (0.30), residues: 707 helix: -0.21 (0.25), residues: 407 sheet: -0.39 (0.74), residues: 50 loop : -2.96 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 450 TYR 0.017 0.002 TYR B 172 PHE 0.022 0.002 PHE A 347 TRP 0.005 0.001 TRP B 314 HIS 0.022 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 5795) covalent geometry : angle 0.64846 ( 7813) hydrogen bonds : bond 0.05903 ( 340) hydrogen bonds : angle 6.58565 ( 1011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9135 (t0) cc_final: 0.8615 (p0) REVERT: A 135 VAL cc_start: 0.8405 (t) cc_final: 0.8155 (t) REVERT: A 164 CYS cc_start: 0.9219 (m) cc_final: 0.8796 (p) REVERT: A 168 GLU cc_start: 0.7080 (tt0) cc_final: 0.6368 (tp30) REVERT: A 179 ASP cc_start: 0.9057 (t0) cc_final: 0.8705 (t0) REVERT: A 212 TYR cc_start: 0.9119 (p90) cc_final: 0.8877 (p90) REVERT: A 337 ILE cc_start: 0.9464 (mt) cc_final: 0.9261 (tp) REVERT: B 142 GLN cc_start: 0.9260 (tt0) cc_final: 0.8833 (tt0) REVERT: B 223 MET cc_start: 0.7021 (mmt) cc_final: 0.6545 (mmm) REVERT: B 258 GLN cc_start: 0.9226 (tp40) cc_final: 0.8979 (tp-100) REVERT: B 268 GLU cc_start: 0.9297 (tt0) cc_final: 0.8705 (tt0) REVERT: B 306 ARG cc_start: 0.8728 (ptt180) cc_final: 0.8440 (ptt180) REVERT: B 329 MET cc_start: 0.5290 (mpp) cc_final: 0.5080 (mpp) REVERT: B 389 PHE cc_start: 0.8992 (m-80) cc_final: 0.8767 (m-80) REVERT: B 484 MET cc_start: 0.8333 (tmm) cc_final: 0.8100 (tmm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1738 time to fit residues: 32.0864 Evaluate side-chains 122 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 142 GLN B 143 ASN B 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.081335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064135 restraints weight = 81647.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067540 restraints weight = 46302.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070054 restraints weight = 30005.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071877 restraints weight = 21082.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.073231 restraints weight = 15723.674| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5795 Z= 0.255 Angle : 0.679 7.692 7813 Z= 0.403 Chirality : 0.039 0.137 871 Planarity : 0.006 0.063 1007 Dihedral : 6.030 49.717 786 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.73 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -2.07 (0.30), residues: 707 helix: -0.40 (0.24), residues: 406 sheet: -0.59 (0.72), residues: 50 loop : -3.17 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 450 TYR 0.022 0.002 TYR B 317 PHE 0.024 0.002 PHE B 389 TRP 0.010 0.002 TRP B 314 HIS 0.016 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5795) covalent geometry : angle 0.67899 ( 7813) hydrogen bonds : bond 0.05830 ( 340) hydrogen bonds : angle 6.63245 ( 1011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 VAL cc_start: 0.8452 (t) cc_final: 0.8201 (t) REVERT: A 164 CYS cc_start: 0.9203 (m) cc_final: 0.8803 (p) REVERT: A 179 ASP cc_start: 0.9033 (t0) cc_final: 0.8651 (t0) REVERT: A 252 GLU cc_start: 0.9280 (mm-30) cc_final: 0.9078 (mm-30) REVERT: B 142 GLN cc_start: 0.9260 (tt0) cc_final: 0.8908 (tt0) REVERT: B 223 MET cc_start: 0.7137 (mmt) cc_final: 0.6629 (mmm) REVERT: B 258 GLN cc_start: 0.9172 (tp40) cc_final: 0.8956 (tp-100) REVERT: B 259 PHE cc_start: 0.9649 (t80) cc_final: 0.9108 (t80) REVERT: B 268 GLU cc_start: 0.9222 (tt0) cc_final: 0.8671 (tt0) REVERT: B 316 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9209 (mtpt) REVERT: B 389 PHE cc_start: 0.9043 (m-80) cc_final: 0.8828 (m-10) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1555 time to fit residues: 28.3546 Evaluate side-chains 115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066241 restraints weight = 75844.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069825 restraints weight = 42489.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072554 restraints weight = 27263.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.074591 restraints weight = 18943.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076102 restraints weight = 13919.792| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5795 Z= 0.152 Angle : 0.580 10.507 7813 Z= 0.334 Chirality : 0.038 0.140 871 Planarity : 0.004 0.063 1007 Dihedral : 5.591 41.491 786 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.48 (0.31), residues: 707 helix: 0.18 (0.25), residues: 417 sheet: -0.71 (0.65), residues: 60 loop : -3.24 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.019 0.001 TYR B 383 PHE 0.024 0.002 PHE B 396 TRP 0.009 0.002 TRP A 219 HIS 0.012 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5795) covalent geometry : angle 0.58024 ( 7813) hydrogen bonds : bond 0.05284 ( 340) hydrogen bonds : angle 6.09880 ( 1011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9136 (t0) cc_final: 0.8651 (p0) REVERT: A 135 VAL cc_start: 0.8368 (t) cc_final: 0.8123 (t) REVERT: A 164 CYS cc_start: 0.9144 (m) cc_final: 0.8727 (p) REVERT: A 168 GLU cc_start: 0.7086 (tt0) cc_final: 0.6554 (tp30) REVERT: A 179 ASP cc_start: 0.9022 (t0) cc_final: 0.8673 (t0) REVERT: A 252 GLU cc_start: 0.9254 (mm-30) cc_final: 0.9026 (mm-30) REVERT: B 142 GLN cc_start: 0.9202 (tt0) cc_final: 0.8954 (tt0) REVERT: B 150 SER cc_start: 0.9424 (t) cc_final: 0.9221 (p) REVERT: B 223 MET cc_start: 0.7040 (mmt) cc_final: 0.6516 (mmm) REVERT: B 258 GLN cc_start: 0.9162 (tp40) cc_final: 0.8944 (tp-100) REVERT: B 259 PHE cc_start: 0.9638 (t80) cc_final: 0.9062 (t80) REVERT: B 268 GLU cc_start: 0.9219 (tt0) cc_final: 0.8641 (tt0) REVERT: B 316 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9102 (mtpt) REVERT: B 389 PHE cc_start: 0.9007 (m-80) cc_final: 0.8746 (m-10) REVERT: B 410 PHE cc_start: 0.8877 (m-10) cc_final: 0.8665 (m-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1504 time to fit residues: 27.9002 Evaluate side-chains 117 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066536 restraints weight = 75241.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070113 restraints weight = 42673.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072891 restraints weight = 27620.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074929 restraints weight = 19297.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.076473 restraints weight = 14317.076| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5795 Z= 0.139 Angle : 0.528 5.779 7813 Z= 0.310 Chirality : 0.037 0.144 871 Planarity : 0.004 0.062 1007 Dihedral : 5.379 39.266 786 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.15 (0.31), residues: 707 helix: 0.51 (0.25), residues: 418 sheet: -0.43 (0.68), residues: 60 loop : -3.32 (0.35), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.014 0.001 TYR B 383 PHE 0.021 0.002 PHE A 140 TRP 0.006 0.001 TRP B 314 HIS 0.011 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5795) covalent geometry : angle 0.52845 ( 7813) hydrogen bonds : bond 0.04951 ( 340) hydrogen bonds : angle 5.80567 ( 1011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9169 (t0) cc_final: 0.8671 (p0) REVERT: A 135 VAL cc_start: 0.8254 (t) cc_final: 0.7984 (t) REVERT: A 164 CYS cc_start: 0.9072 (m) cc_final: 0.8769 (p) REVERT: A 168 GLU cc_start: 0.7091 (tt0) cc_final: 0.6517 (tp30) REVERT: A 179 ASP cc_start: 0.9067 (t0) cc_final: 0.8717 (t0) REVERT: A 252 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8996 (mm-30) REVERT: B 142 GLN cc_start: 0.9128 (tt0) cc_final: 0.8889 (tt0) REVERT: B 223 MET cc_start: 0.7004 (mmt) cc_final: 0.6584 (mmm) REVERT: B 258 GLN cc_start: 0.9131 (tp40) cc_final: 0.8925 (tp-100) REVERT: B 259 PHE cc_start: 0.9640 (t80) cc_final: 0.9077 (t80) REVERT: B 268 GLU cc_start: 0.9216 (tt0) cc_final: 0.8599 (tt0) REVERT: B 322 MET cc_start: 0.9205 (mmm) cc_final: 0.8908 (mmm) REVERT: B 369 GLU cc_start: 0.9369 (mp0) cc_final: 0.9158 (mp0) REVERT: B 389 PHE cc_start: 0.8999 (m-80) cc_final: 0.8681 (m-10) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1497 time to fit residues: 27.4606 Evaluate side-chains 120 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068764 restraints weight = 72644.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072443 restraints weight = 40879.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.075218 restraints weight = 26320.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077293 restraints weight = 18406.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.078710 restraints weight = 13628.057| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5795 Z= 0.117 Angle : 0.499 6.104 7813 Z= 0.288 Chirality : 0.037 0.141 871 Planarity : 0.004 0.063 1007 Dihedral : 5.074 36.137 786 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.19 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -0.72 (0.32), residues: 707 helix: 0.89 (0.25), residues: 418 sheet: -0.24 (0.70), residues: 60 loop : -3.24 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.018 0.001 TYR B 317 PHE 0.018 0.002 PHE B 430 TRP 0.009 0.001 TRP B 6 HIS 0.009 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 5795) covalent geometry : angle 0.49871 ( 7813) hydrogen bonds : bond 0.04657 ( 340) hydrogen bonds : angle 5.47656 ( 1011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9124 (t0) cc_final: 0.8627 (p0) REVERT: A 164 CYS cc_start: 0.8998 (m) cc_final: 0.8745 (p) REVERT: A 168 GLU cc_start: 0.7084 (tt0) cc_final: 0.6471 (tp30) REVERT: A 179 ASP cc_start: 0.9010 (t0) cc_final: 0.8658 (t0) REVERT: A 252 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8951 (mm-30) REVERT: B 223 MET cc_start: 0.7000 (mmt) cc_final: 0.6469 (mmm) REVERT: B 258 GLN cc_start: 0.9107 (tp40) cc_final: 0.8842 (tp-100) REVERT: B 259 PHE cc_start: 0.9614 (t80) cc_final: 0.9026 (t80) REVERT: B 268 GLU cc_start: 0.9163 (tt0) cc_final: 0.8509 (tt0) REVERT: B 389 PHE cc_start: 0.8896 (m-80) cc_final: 0.8599 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1589 time to fit residues: 28.9731 Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 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 = 0.3556 r_free = 0.3556 target = 0.084965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066323 restraints weight = 77067.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.070027 restraints weight = 43089.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072802 restraints weight = 27578.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.074858 restraints weight = 19155.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076394 restraints weight = 14136.056| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5795 Z= 0.179 Angle : 0.551 5.765 7813 Z= 0.329 Chirality : 0.037 0.130 871 Planarity : 0.005 0.065 1007 Dihedral : 5.265 42.386 786 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.61 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.06 (0.31), residues: 707 helix: 0.61 (0.25), residues: 417 sheet: -0.37 (0.68), residues: 60 loop : -3.37 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.016 0.001 TYR B 481 PHE 0.016 0.002 PHE B 430 TRP 0.005 0.001 TRP B 314 HIS 0.009 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5795) covalent geometry : angle 0.55057 ( 7813) hydrogen bonds : bond 0.04787 ( 340) hydrogen bonds : angle 5.76690 ( 1011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 266 is missing expected H atoms. Skipping. Residue SER 269 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue THR 275 is missing expected H atoms. Skipping. Residue MET 280 is missing expected H atoms. Skipping. Residue LEU 282 is missing expected H atoms. Skipping. Residue LYS 283 is missing expected H atoms. Skipping. Residue ILE 288 is missing expected H atoms. Skipping. Residue SER 291 is missing expected H atoms. Skipping. Residue LEU 292 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue VAL 298 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 VAL cc_start: 0.8140 (t) cc_final: 0.7919 (t) REVERT: A 164 CYS cc_start: 0.9076 (m) cc_final: 0.8771 (p) REVERT: A 168 GLU cc_start: 0.7165 (tt0) cc_final: 0.6532 (tp30) REVERT: A 179 ASP cc_start: 0.9124 (t0) cc_final: 0.8812 (t0) REVERT: A 252 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9030 (mm-30) REVERT: B 223 MET cc_start: 0.6947 (mmt) cc_final: 0.6521 (mmm) REVERT: B 258 GLN cc_start: 0.9178 (tp40) cc_final: 0.8939 (tp-100) REVERT: B 259 PHE cc_start: 0.9663 (t80) cc_final: 0.9141 (t80) REVERT: B 265 CYS cc_start: 0.9035 (t) cc_final: 0.8796 (t) REVERT: B 268 GLU cc_start: 0.9293 (tt0) cc_final: 0.8654 (tt0) REVERT: B 322 MET cc_start: 0.9201 (mmm) cc_final: 0.8925 (mmm) REVERT: B 389 PHE cc_start: 0.9087 (m-80) cc_final: 0.8794 (m-10) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1673 time to fit residues: 28.9802 Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN B 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.084394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.066162 restraints weight = 74722.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.069779 restraints weight = 41798.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072502 restraints weight = 26790.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.074558 restraints weight = 18635.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.076013 restraints weight = 13708.514| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5795 Z= 0.160 Angle : 0.540 5.784 7813 Z= 0.318 Chirality : 0.037 0.131 871 Planarity : 0.004 0.065 1007 Dihedral : 5.233 39.674 786 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.33 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: -1.11 (0.31), residues: 707 helix: 0.57 (0.25), residues: 417 sheet: -0.29 (0.69), residues: 60 loop : -3.40 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 450 TYR 0.019 0.001 TYR B 481 PHE 0.017 0.002 PHE B 430 TRP 0.006 0.001 TRP B 6 HIS 0.008 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5795) covalent geometry : angle 0.54040 ( 7813) hydrogen bonds : bond 0.04733 ( 340) hydrogen bonds : angle 5.71601 ( 1011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.24 seconds wall clock time: 34 minutes 51.76 seconds (2091.76 seconds total)