Starting phenix.real_space_refine on Sun Dec 29 21:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryp_24744/12_2024/7ryp_24744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryp_24744/12_2024/7ryp_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_24744/12_2024/7ryp_24744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryp_24744/12_2024/7ryp_24744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ryp_24744/12_2024/7ryp_24744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryp_24744/12_2024/7ryp_24744.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: 5.69, per 1000 atoms: 0.50 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: 2.82 Conformation dependent library (CDL) restraints added in 835.4 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: 0.80 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: 3.65 Time building geometry restraints manager: 3.39 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: 2.900 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.800 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- 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= 0.971 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.007 TRP B 314 HIS 0.006 0.001 HIS B 419 PHE 0.027 0.005 PHE B 410 TYR 0.053 0.007 TYR A 212 ARG 0.006 0.001 ARG A 34 *********************** 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 : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9050 (t0) cc_final: 0.8708 (p0) REVERT: A 179 ASP cc_start: 0.8972 (t0) cc_final: 0.8583 (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: 0.8833 (pm20) REVERT: A 372 ASP cc_start: 0.9300 (t70) cc_final: 0.9083 (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: 0.8667 (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: 0.4108 time to fit residues: 98.1277 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 : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5795 Z= 0.201 Angle : 0.678 8.319 7813 Z= 0.388 Chirality : 0.041 0.175 871 Planarity : 0.005 0.056 1007 Dihedral : 5.738 50.187 786 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.20 % Favored : 91.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.30), residues: 707 helix: 0.16 (0.24), residues: 412 sheet: -0.82 (0.61), residues: 63 loop : -2.49 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 6 HIS 0.006 0.002 HIS B 426 PHE 0.022 0.002 PHE A 347 TYR 0.016 0.002 TYR B 169 ARG 0.003 0.000 ARG A 138 *********************** 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 177 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.950 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: A 135 VAL cc_start: 0.8280 (t) cc_final: 0.8057 (t) REVERT: A 164 CYS cc_start: 0.9146 (m) cc_final: 0.8843 (m) REVERT: A 179 ASP cc_start: 0.9044 (t0) cc_final: 0.8697 (t0) REVERT: A 262 ASN cc_start: 0.9300 (m-40) cc_final: 0.8980 (m-40) REVERT: A 371 GLU cc_start: 0.9442 (tt0) cc_final: 0.8890 (pm20) REVERT: B 94 LEU cc_start: 0.9391 (mt) cc_final: 0.9147 (mt) REVERT: B 142 GLN cc_start: 0.9210 (tt0) cc_final: 0.8764 (tt0) REVERT: B 265 CYS cc_start: 0.9236 (t) cc_final: 0.9017 (t) REVERT: B 268 GLU cc_start: 0.9084 (tt0) cc_final: 0.8347 (tt0) REVERT: B 322 MET cc_start: 0.9712 (mmp) cc_final: 0.9438 (mmm) REVERT: B 443 ARG cc_start: 0.9607 (ttp80) cc_final: 0.9251 (mtm110) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.3786 time to fit residues: 86.0268 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 : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5795 Z= 0.231 Angle : 0.633 9.604 7813 Z= 0.372 Chirality : 0.039 0.150 871 Planarity : 0.005 0.060 1007 Dihedral : 5.596 51.211 786 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.34 % Favored : 90.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.30), residues: 707 helix: 0.25 (0.24), residues: 410 sheet: -0.64 (0.62), residues: 65 loop : -2.48 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 249 HIS 0.011 0.002 HIS A 341 PHE 0.019 0.002 PHE A 347 TYR 0.018 0.002 TYR B 172 ARG 0.004 0.000 ARG B 442 *********************** 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 160 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.831 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: A 135 VAL cc_start: 0.8334 (t) cc_final: 0.8080 (t) REVERT: A 164 CYS cc_start: 0.9109 (m) cc_final: 0.8565 (p) REVERT: A 168 GLU cc_start: 0.7424 (tt0) cc_final: 0.7059 (tp30) REVERT: A 179 ASP cc_start: 0.9011 (t0) cc_final: 0.8636 (t0) REVERT: A 250 SER cc_start: 0.8470 (t) cc_final: 0.8093 (t) REVERT: B 94 LEU cc_start: 0.9474 (mt) cc_final: 0.9255 (mt) REVERT: B 142 GLN cc_start: 0.9249 (tt0) cc_final: 0.8899 (tt0) REVERT: B 258 GLN cc_start: 0.9287 (tp40) cc_final: 0.8687 (tp-100) REVERT: B 259 PHE cc_start: 0.9325 (t80) cc_final: 0.9106 (t80) REVERT: B 262 ASN cc_start: 0.9006 (m-40) cc_final: 0.8688 (m110) REVERT: B 268 GLU cc_start: 0.9113 (tt0) cc_final: 0.8572 (tt0) REVERT: B 426 HIS cc_start: 0.9180 (t70) cc_final: 0.8954 (t-170) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3921 time to fit residues: 80.5685 Evaluate side-chains 137 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5795 Z= 0.163 Angle : 0.556 9.374 7813 Z= 0.319 Chirality : 0.038 0.155 871 Planarity : 0.004 0.061 1007 Dihedral : 5.333 42.707 786 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.48 % Favored : 90.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.31), residues: 707 helix: 0.57 (0.25), residues: 407 sheet: -0.49 (0.64), residues: 65 loop : -2.47 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 314 HIS 0.006 0.001 HIS B 271 PHE 0.021 0.002 PHE B 396 TYR 0.024 0.001 TYR B 317 ARG 0.002 0.000 ARG B 450 *********************** 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 161 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.904 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: 0.9121 (t0) cc_final: 0.8578 (p0) REVERT: A 164 CYS cc_start: 0.9100 (m) cc_final: 0.8596 (p) REVERT: A 168 GLU cc_start: 0.7453 (tt0) cc_final: 0.6858 (tp30) REVERT: A 179 ASP cc_start: 0.9091 (t0) cc_final: 0.8779 (t0) REVERT: A 212 TYR cc_start: 0.8996 (p90) cc_final: 0.8734 (p90) REVERT: A 252 GLU cc_start: 0.8085 (mp0) cc_final: 0.7794 (mp0) REVERT: B 142 GLN cc_start: 0.9222 (tt0) cc_final: 0.8907 (tt0) REVERT: B 259 PHE cc_start: 0.9345 (t80) cc_final: 0.9077 (t80) REVERT: B 268 GLU cc_start: 0.9216 (tt0) cc_final: 0.8483 (tt0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.3979 time to fit residues: 82.1583 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5795 Z= 0.196 Angle : 0.580 10.951 7813 Z= 0.335 Chirality : 0.037 0.146 871 Planarity : 0.004 0.061 1007 Dihedral : 5.348 45.590 786 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.04 % Favored : 89.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 707 helix: 0.50 (0.25), residues: 407 sheet: -0.30 (0.65), residues: 65 loop : -2.59 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 219 HIS 0.017 0.002 HIS B 426 PHE 0.019 0.002 PHE A 347 TYR 0.015 0.001 TYR B 383 ARG 0.003 0.000 ARG B 385 *********************** 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 148 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.836 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: A 79 ASP cc_start: 0.9138 (t0) cc_final: 0.8589 (p0) REVERT: A 164 CYS cc_start: 0.9107 (m) cc_final: 0.8703 (p) REVERT: A 168 GLU cc_start: 0.7315 (tt0) cc_final: 0.6628 (tp30) REVERT: A 179 ASP cc_start: 0.9088 (t0) cc_final: 0.8723 (t0) REVERT: A 212 TYR cc_start: 0.8923 (p90) cc_final: 0.8612 (p90) REVERT: B 142 GLN cc_start: 0.9313 (tt0) cc_final: 0.8988 (tt0) REVERT: B 210 ASN cc_start: 0.9719 (m110) cc_final: 0.9507 (m110) REVERT: B 259 PHE cc_start: 0.9375 (t80) cc_final: 0.9101 (t80) REVERT: B 268 GLU cc_start: 0.9129 (tt0) cc_final: 0.8637 (tt0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3792 time to fit residues: 72.5310 Evaluate side-chains 131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.0020 chunk 36 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- 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 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5137 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= 0.165 Angle : 0.540 9.062 7813 Z= 0.311 Chirality : 0.037 0.140 871 Planarity : 0.004 0.061 1007 Dihedral : 5.265 42.427 786 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.62 % Favored : 90.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.32), residues: 707 helix: 0.82 (0.25), residues: 402 sheet: -0.17 (0.67), residues: 65 loop : -2.49 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 219 HIS 0.013 0.002 HIS B 426 PHE 0.019 0.002 PHE A 347 TYR 0.014 0.001 TYR B 383 ARG 0.003 0.000 ARG B 450 *********************** 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 142 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.914 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: A 79 ASP cc_start: 0.9104 (t0) cc_final: 0.8553 (p0) REVERT: A 164 CYS cc_start: 0.9081 (m) cc_final: 0.8738 (p) REVERT: A 168 GLU cc_start: 0.7300 (tt0) cc_final: 0.6705 (tp30) REVERT: A 179 ASP cc_start: 0.9057 (t0) cc_final: 0.8669 (t0) REVERT: A 212 TYR cc_start: 0.8915 (p90) cc_final: 0.8602 (p90) REVERT: A 252 GLU cc_start: 0.8212 (mp0) cc_final: 0.7947 (mp0) REVERT: B 142 GLN cc_start: 0.9326 (tt0) cc_final: 0.8910 (tt0) REVERT: B 259 PHE cc_start: 0.9434 (t80) cc_final: 0.9105 (t80) REVERT: B 268 GLU cc_start: 0.9177 (tt0) cc_final: 0.8652 (tt0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3937 time to fit residues: 72.1414 Evaluate side-chains 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN B 143 ASN B 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5795 Z= 0.152 Angle : 0.528 8.811 7813 Z= 0.303 Chirality : 0.037 0.139 871 Planarity : 0.004 0.065 1007 Dihedral : 5.113 40.275 786 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.32), residues: 707 helix: 0.96 (0.26), residues: 408 sheet: -0.16 (0.71), residues: 60 loop : -2.46 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.011 0.001 HIS B 426 PHE 0.019 0.002 PHE A 347 TYR 0.011 0.001 TYR B 169 ARG 0.003 0.000 ARG B 385 *********************** 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 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.066 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: A 79 ASP cc_start: 0.9124 (t0) cc_final: 0.8569 (p0) REVERT: A 164 CYS cc_start: 0.9075 (m) cc_final: 0.8721 (p) REVERT: A 168 GLU cc_start: 0.7237 (tt0) cc_final: 0.6715 (tp30) REVERT: A 179 ASP cc_start: 0.9048 (t0) cc_final: 0.8654 (t0) REVERT: A 212 TYR cc_start: 0.8915 (p90) cc_final: 0.8597 (p90) REVERT: A 252 GLU cc_start: 0.8138 (mp0) cc_final: 0.7921 (mp0) REVERT: B 142 GLN cc_start: 0.9255 (tt0) cc_final: 0.8869 (tt0) REVERT: B 259 PHE cc_start: 0.9421 (t80) cc_final: 0.9085 (t80) REVERT: B 268 GLU cc_start: 0.9283 (tt0) cc_final: 0.8541 (tt0) REVERT: B 410 PHE cc_start: 0.8854 (m-80) cc_final: 0.8563 (m-10) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3924 time to fit residues: 72.4437 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5795 Z= 0.332 Angle : 0.693 8.550 7813 Z= 0.412 Chirality : 0.038 0.133 871 Planarity : 0.005 0.060 1007 Dihedral : 5.648 46.821 786 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.46 % Favored : 88.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.30), residues: 707 helix: 0.17 (0.25), residues: 402 sheet: -0.05 (0.75), residues: 49 loop : -2.85 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 249 HIS 0.013 0.002 HIS B 426 PHE 0.022 0.003 PHE A 347 TYR 0.020 0.002 TYR B 172 ARG 0.010 0.001 ARG B 385 *********************** 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 144 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.968 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: A 164 CYS cc_start: 0.9090 (m) cc_final: 0.8827 (p) REVERT: A 179 ASP cc_start: 0.9102 (t0) cc_final: 0.8773 (t0) REVERT: A 212 TYR cc_start: 0.8945 (p90) cc_final: 0.8674 (p90) REVERT: A 252 GLU cc_start: 0.8269 (mp0) cc_final: 0.8061 (mp0) REVERT: B 142 GLN cc_start: 0.9278 (tt0) cc_final: 0.8965 (tt0) REVERT: B 216 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8817 (mm110) REVERT: B 258 GLN cc_start: 0.9158 (tp40) cc_final: 0.8917 (tp-100) REVERT: B 259 PHE cc_start: 0.9428 (t80) cc_final: 0.9108 (t80) REVERT: B 268 GLU cc_start: 0.9268 (tt0) cc_final: 0.8797 (tt0) REVERT: B 306 ARG cc_start: 0.8849 (ptt180) cc_final: 0.8642 (ptt180) REVERT: B 426 HIS cc_start: 0.9269 (t70) cc_final: 0.9052 (t-170) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.4039 time to fit residues: 74.5333 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5772 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= 0.168 Angle : 0.546 10.197 7813 Z= 0.312 Chirality : 0.037 0.138 871 Planarity : 0.004 0.065 1007 Dihedral : 5.314 40.486 786 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 707 helix: 0.65 (0.25), residues: 401 sheet: 0.10 (0.76), residues: 49 loop : -2.74 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 219 HIS 0.011 0.001 HIS B 426 PHE 0.021 0.002 PHE A 347 TYR 0.019 0.001 TYR B 317 ARG 0.008 0.000 ARG B 385 *********************** 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 : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.9128 (t0) cc_final: 0.8624 (p0) REVERT: A 164 CYS cc_start: 0.8977 (m) cc_final: 0.8766 (p) REVERT: A 168 GLU cc_start: 0.7109 (tt0) cc_final: 0.6524 (tp30) REVERT: A 179 ASP cc_start: 0.9068 (t0) cc_final: 0.8715 (t0) REVERT: A 212 TYR cc_start: 0.8905 (p90) cc_final: 0.8630 (p90) REVERT: A 252 GLU cc_start: 0.8239 (mp0) cc_final: 0.8030 (mp0) REVERT: B 116 GLU cc_start: 0.9560 (pt0) cc_final: 0.9322 (pt0) REVERT: B 142 GLN cc_start: 0.9251 (tt0) cc_final: 0.8909 (tt0) REVERT: B 258 GLN cc_start: 0.9071 (tp40) cc_final: 0.8847 (tp-100) REVERT: B 259 PHE cc_start: 0.9408 (t80) cc_final: 0.9073 (t80) REVERT: B 268 GLU cc_start: 0.9185 (tt0) cc_final: 0.8688 (tt0) REVERT: B 410 PHE cc_start: 0.8736 (m-10) cc_final: 0.8516 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3893 time to fit residues: 70.3745 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 : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5795 Z= 0.204 Angle : 0.574 9.291 7813 Z= 0.335 Chirality : 0.037 0.147 871 Planarity : 0.004 0.065 1007 Dihedral : 5.381 46.160 786 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.31), residues: 707 helix: 0.49 (0.25), residues: 408 sheet: 0.40 (0.87), residues: 39 loop : -2.85 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 219 HIS 0.011 0.002 HIS B 426 PHE 0.020 0.002 PHE A 347 TYR 0.018 0.001 TYR B 317 ARG 0.004 0.000 ARG B 450 ********************** 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 138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9157 (t0) cc_final: 0.8628 (p0) REVERT: A 168 GLU cc_start: 0.7115 (tt0) cc_final: 0.6595 (tp30) REVERT: A 179 ASP cc_start: 0.9131 (t0) cc_final: 0.8746 (t0) REVERT: A 212 TYR cc_start: 0.8902 (p90) cc_final: 0.8637 (p90) REVERT: B 142 GLN cc_start: 0.9216 (tt0) cc_final: 0.8937 (tt0) REVERT: B 258 GLN cc_start: 0.9110 (tp40) cc_final: 0.8882 (tp-100) REVERT: B 259 PHE cc_start: 0.9439 (t80) cc_final: 0.9123 (t80) REVERT: B 268 GLU cc_start: 0.9332 (tt0) cc_final: 0.8678 (tt0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4760 time to fit residues: 85.1945 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 140 GLN B 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.083850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066827 restraints weight = 75026.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070346 restraints weight = 41832.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072964 restraints weight = 26764.190| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5795 Z= 0.237 Angle : 0.607 9.467 7813 Z= 0.355 Chirality : 0.038 0.143 871 Planarity : 0.005 0.064 1007 Dihedral : 5.593 46.172 786 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.30), residues: 707 helix: 0.23 (0.25), residues: 406 sheet: 0.25 (0.85), residues: 39 loop : -2.92 (0.33), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 314 HIS 0.011 0.002 HIS B 426 PHE 0.023 0.002 PHE A 347 TYR 0.019 0.002 TYR B 383 ARG 0.006 0.001 ARG B 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.46 seconds wall clock time: 54 minutes 23.84 seconds (3263.84 seconds total)