Starting phenix.real_space_refine on Fri Mar 15 09:39:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_2024/7ryp_24744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_2024/7ryp_24744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_2024/7ryp_24744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_2024/7ryp_24744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryp_24744/03_2024/7ryp_24744.pdb" } 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 Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.29, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 9.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.02 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: 3.82 Time building geometry restraints manager: 9.54 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: 95.42 - 103.12: 43 103.12 - 110.82: 11899 110.82 - 118.52: 2993 118.52 - 126.22: 5435 126.22 - 133.92: 103 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 1.850 nonbonded pdb=" OE1 GLU B 225 " pdb=" H GLU B 225 " model vdw 1.265 1.850 nonbonded pdb=" OE1 GLU B 248 " pdb=" H GLU B 248 " model vdw 1.306 1.850 nonbonded pdb=" OE1 GLU B 204 " pdb=" H GLU B 204 " model vdw 1.335 1.850 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.342 1.850 ... (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 ========== 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: 1.370 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 5.980 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.012 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: 0.4020 time to fit residues: 95.3919 Evaluate side-chains 144 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5795 Z= 0.195 Angle : 0.660 7.694 7813 Z= 0.380 Chirality : 0.040 0.170 871 Planarity : 0.004 0.056 1007 Dihedral : 5.594 39.468 786 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.92 % 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 (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: -1.09 (0.30), residues: 707 helix: 0.19 (0.24), residues: 411 sheet: -0.63 (0.60), residues: 63 loop : -2.36 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 6 HIS 0.006 0.001 HIS B 426 PHE 0.022 0.002 PHE A 347 TYR 0.017 0.002 TYR B 169 ARG 0.003 0.000 ARG A 235 *********************** 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 176 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.081 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 79 ASP cc_start: 0.9088 (t0) cc_final: 0.8532 (p0) REVERT: A 135 VAL cc_start: 0.8273 (t) cc_final: 0.8059 (t) REVERT: A 164 CYS cc_start: 0.9160 (m) cc_final: 0.8850 (m) REVERT: A 179 ASP cc_start: 0.8975 (t0) cc_final: 0.8613 (t0) REVERT: A 256 ILE cc_start: 0.8903 (mt) cc_final: 0.8630 (mt) REVERT: A 262 ASN cc_start: 0.9268 (m-40) cc_final: 0.9017 (m-40) REVERT: A 371 GLU cc_start: 0.9468 (tt0) cc_final: 0.8789 (pm20) REVERT: A 372 ASP cc_start: 0.9232 (t70) cc_final: 0.8985 (t0) REVERT: B 94 LEU cc_start: 0.9390 (mt) cc_final: 0.9145 (mt) REVERT: B 142 GLN cc_start: 0.9151 (tt0) cc_final: 0.8704 (tt0) REVERT: B 259 PHE cc_start: 0.9223 (t80) cc_final: 0.8800 (t80) REVERT: B 265 CYS cc_start: 0.9229 (t) cc_final: 0.8981 (t) REVERT: B 268 GLU cc_start: 0.9095 (tt0) cc_final: 0.8462 (tt0) REVERT: B 322 MET cc_start: 0.9711 (mmp) cc_final: 0.9464 (mmm) REVERT: B 440 MET cc_start: 0.9185 (mmt) cc_final: 0.8330 (mpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3637 time to fit residues: 82.7079 Evaluate side-chains 144 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 209 HIS B 324 ASN B 464 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5795 Z= 0.191 Angle : 0.581 6.019 7813 Z= 0.342 Chirality : 0.038 0.153 871 Planarity : 0.004 0.057 1007 Dihedral : 5.374 34.011 786 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.19 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.87 (0.31), residues: 707 helix: 0.41 (0.25), residues: 410 sheet: -0.72 (0.65), residues: 60 loop : -2.25 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 249 HIS 0.007 0.001 HIS A 341 PHE 0.020 0.002 PHE A 347 TYR 0.015 0.001 TYR B 172 ARG 0.003 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 159 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.024 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: A 79 ASP cc_start: 0.8989 (t0) cc_final: 0.8400 (p0) REVERT: A 135 VAL cc_start: 0.8288 (t) cc_final: 0.8076 (t) REVERT: A 164 CYS cc_start: 0.9106 (m) cc_final: 0.8544 (p) REVERT: A 179 ASP cc_start: 0.8992 (t0) cc_final: 0.8641 (t0) REVERT: A 371 GLU cc_start: 0.9491 (tt0) cc_final: 0.8866 (pm20) REVERT: B 142 GLN cc_start: 0.9171 (tt0) cc_final: 0.8769 (tt0) REVERT: B 237 ARG cc_start: 0.9307 (mmm-85) cc_final: 0.8971 (tpt-90) REVERT: B 268 GLU cc_start: 0.9146 (tt0) cc_final: 0.8638 (tt0) REVERT: B 389 PHE cc_start: 0.8603 (m-80) cc_final: 0.8383 (m-80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3808 time to fit residues: 78.7804 Evaluate side-chains 132 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 B 143 ASN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN B 332 ASN B 470 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5795 Z= 0.240 Angle : 0.623 12.064 7813 Z= 0.364 Chirality : 0.038 0.147 871 Planarity : 0.004 0.061 1007 Dihedral : 5.325 28.944 786 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.68 % 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 (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: -1.02 (0.31), residues: 707 helix: 0.32 (0.25), residues: 411 sheet: -0.62 (0.68), residues: 60 loop : -2.46 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 149 HIS 0.007 0.002 HIS B 105 PHE 0.020 0.002 PHE A 347 TYR 0.017 0.002 TYR B 172 ARG 0.005 0.001 ARG B 385 *********************** 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 156 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.937 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: 0.9077 (t0) cc_final: 0.8464 (p0) REVERT: A 164 CYS cc_start: 0.9194 (m) cc_final: 0.8660 (p) REVERT: A 168 GLU cc_start: 0.7231 (tt0) cc_final: 0.6759 (tp30) REVERT: A 179 ASP cc_start: 0.9012 (t0) cc_final: 0.8637 (t0) REVERT: A 212 TYR cc_start: 0.9038 (p90) cc_final: 0.8780 (p90) REVERT: A 252 GLU cc_start: 0.8242 (mp0) cc_final: 0.7969 (mp0) REVERT: A 371 GLU cc_start: 0.9515 (tt0) cc_final: 0.9051 (pm20) REVERT: B 142 GLN cc_start: 0.9150 (tt0) cc_final: 0.8783 (tt0) REVERT: B 237 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8939 (tpt-90) REVERT: B 259 PHE cc_start: 0.9526 (t80) cc_final: 0.9149 (t80) REVERT: B 268 GLU cc_start: 0.9135 (tt0) cc_final: 0.8782 (tt0) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3910 time to fit residues: 77.6839 Evaluate side-chains 132 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** 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: 0.7677 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5795 Z= 0.230 Angle : 0.616 10.486 7813 Z= 0.357 Chirality : 0.037 0.140 871 Planarity : 0.004 0.063 1007 Dihedral : 5.355 28.242 786 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.03 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -1.15 (0.31), residues: 707 helix: 0.23 (0.25), residues: 405 sheet: -0.31 (0.68), residues: 60 loop : -2.59 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 314 HIS 0.005 0.001 HIS B 479 PHE 0.021 0.002 PHE B 396 TYR 0.024 0.002 TYR B 317 ARG 0.005 0.001 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 154 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.894 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: 0.9022 (t0) cc_final: 0.8457 (p0) REVERT: A 164 CYS cc_start: 0.9115 (m) cc_final: 0.8746 (p) REVERT: A 168 GLU cc_start: 0.7230 (tt0) cc_final: 0.6698 (tp30) REVERT: A 179 ASP cc_start: 0.9124 (t0) cc_final: 0.8755 (t0) REVERT: A 212 TYR cc_start: 0.8938 (p90) cc_final: 0.8659 (p90) REVERT: A 252 GLU cc_start: 0.8245 (mp0) cc_final: 0.8038 (mp0) REVERT: A 371 GLU cc_start: 0.9503 (tt0) cc_final: 0.9025 (pm20) REVERT: B 142 GLN cc_start: 0.9156 (tt0) cc_final: 0.8810 (tt0) REVERT: B 259 PHE cc_start: 0.9523 (t80) cc_final: 0.9093 (t80) REVERT: B 268 GLU cc_start: 0.9184 (tt0) cc_final: 0.8811 (tt0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3775 time to fit residues: 74.8207 Evaluate side-chains 132 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** 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: 0.7602 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5795 Z= 0.155 Angle : 0.532 10.063 7813 Z= 0.304 Chirality : 0.037 0.139 871 Planarity : 0.004 0.061 1007 Dihedral : 5.145 25.178 786 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.04 % Favored : 89.67 % 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: 0.79 (0.25), residues: 407 sheet: -0.09 (0.69), residues: 60 loop : -2.48 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 219 HIS 0.023 0.002 HIS B 426 PHE 0.046 0.002 PHE B 266 TYR 0.011 0.001 TYR B 169 ARG 0.002 0.000 ARG A 32 *********************** 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 148 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.951 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: A 79 ASP cc_start: 0.9090 (t0) cc_final: 0.8578 (p0) REVERT: A 164 CYS cc_start: 0.9055 (m) cc_final: 0.8656 (p) REVERT: A 168 GLU cc_start: 0.7159 (tt0) cc_final: 0.6720 (tp30) REVERT: A 179 ASP cc_start: 0.8840 (t0) cc_final: 0.8492 (t0) REVERT: A 212 TYR cc_start: 0.8907 (p90) cc_final: 0.8627 (p90) REVERT: A 371 GLU cc_start: 0.9455 (tt0) cc_final: 0.8818 (pm20) REVERT: B 142 GLN cc_start: 0.9120 (tt0) cc_final: 0.8795 (tt0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3938 time to fit residues: 74.5058 Evaluate side-chains 126 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7642 moved from start: 0.5421 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= 0.178 Angle : 0.539 8.264 7813 Z= 0.312 Chirality : 0.037 0.148 871 Planarity : 0.004 0.060 1007 Dihedral : 5.103 28.838 786 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.04 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.51 (0.32), residues: 707 helix: 0.83 (0.25), residues: 408 sheet: 0.42 (0.75), residues: 49 loop : -2.54 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.017 0.002 HIS B 426 PHE 0.021 0.002 PHE B 266 TYR 0.013 0.001 TYR B 317 ARG 0.004 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 146 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.903 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: A 79 ASP cc_start: 0.9067 (t0) cc_final: 0.8513 (p0) REVERT: A 164 CYS cc_start: 0.9064 (m) cc_final: 0.8750 (p) REVERT: A 168 GLU cc_start: 0.7226 (tt0) cc_final: 0.6697 (tp30) REVERT: A 179 ASP cc_start: 0.8937 (t0) cc_final: 0.8555 (t0) REVERT: A 212 TYR cc_start: 0.8894 (p90) cc_final: 0.8630 (p90) REVERT: A 371 GLU cc_start: 0.9455 (tt0) cc_final: 0.8849 (pm20) REVERT: B 142 GLN cc_start: 0.9075 (tt0) cc_final: 0.8867 (tt0) REVERT: B 259 PHE cc_start: 0.9602 (t80) cc_final: 0.9222 (t80) REVERT: B 268 GLU cc_start: 0.9062 (tt0) cc_final: 0.8859 (tt0) REVERT: B 410 PHE cc_start: 0.8909 (m-80) cc_final: 0.8593 (m-10) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3839 time to fit residues: 71.9498 Evaluate side-chains 128 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 7.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7722 moved from start: 0.5714 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= 0.247 Angle : 0.607 6.546 7813 Z= 0.359 Chirality : 0.037 0.139 871 Planarity : 0.005 0.060 1007 Dihedral : 5.345 26.245 786 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.46 % Favored : 88.26 % 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: -1.12 (0.31), residues: 707 helix: 0.32 (0.25), residues: 408 sheet: 0.29 (0.73), residues: 49 loop : -2.79 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 314 HIS 0.013 0.002 HIS B 426 PHE 0.023 0.003 PHE B 266 TYR 0.016 0.002 TYR B 172 ARG 0.009 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 142 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.954 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: 0.9093 (t0) cc_final: 0.8524 (p0) REVERT: A 164 CYS cc_start: 0.9056 (m) cc_final: 0.8792 (p) REVERT: A 179 ASP cc_start: 0.8998 (t0) cc_final: 0.8639 (t0) REVERT: A 212 TYR cc_start: 0.8948 (p90) cc_final: 0.8690 (p90) REVERT: A 371 GLU cc_start: 0.9481 (tt0) cc_final: 0.8961 (pm20) REVERT: B 259 PHE cc_start: 0.9600 (t80) cc_final: 0.9209 (t80) REVERT: B 268 GLU cc_start: 0.9139 (tt0) cc_final: 0.8649 (tt0) REVERT: B 410 PHE cc_start: 0.8981 (m-80) cc_final: 0.8634 (m-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3827 time to fit residues: 69.7634 Evaluate side-chains 117 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 210 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: 0.7655 moved from start: 0.5920 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= 0.158 Angle : 0.511 6.581 7813 Z= 0.298 Chirality : 0.037 0.157 871 Planarity : 0.004 0.061 1007 Dihedral : 5.062 24.933 786 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.32 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: -0.65 (0.31), residues: 707 helix: 0.73 (0.25), residues: 409 sheet: 0.38 (0.73), residues: 49 loop : -2.65 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 219 HIS 0.012 0.001 HIS B 426 PHE 0.034 0.002 PHE B 266 TYR 0.018 0.001 TYR B 317 ARG 0.002 0.000 ARG A 32 *********************** 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 137 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.907 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: A 32 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7996 (ttt-90) REVERT: A 79 ASP cc_start: 0.9140 (t0) cc_final: 0.8618 (p0) REVERT: A 164 CYS cc_start: 0.8980 (m) cc_final: 0.8748 (p) REVERT: A 168 GLU cc_start: 0.7145 (tt0) cc_final: 0.6535 (tp30) REVERT: A 179 ASP cc_start: 0.8912 (t0) cc_final: 0.8534 (t0) REVERT: A 212 TYR cc_start: 0.8875 (p90) cc_final: 0.8616 (p90) REVERT: A 371 GLU cc_start: 0.9437 (tt0) cc_final: 0.8842 (pm20) REVERT: B 259 PHE cc_start: 0.9587 (t80) cc_final: 0.9278 (t80) REVERT: B 268 GLU cc_start: 0.9041 (tt0) cc_final: 0.8797 (tt0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3838 time to fit residues: 68.4454 Evaluate side-chains 116 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7685 moved from start: 0.6093 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= 0.191 Angle : 0.535 6.001 7813 Z= 0.316 Chirality : 0.037 0.160 871 Planarity : 0.004 0.060 1007 Dihedral : 5.100 27.236 786 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.17 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.77 (0.31), residues: 707 helix: 0.67 (0.25), residues: 410 sheet: 0.37 (0.73), residues: 49 loop : -2.80 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 219 HIS 0.010 0.001 HIS B 426 PHE 0.025 0.002 PHE B 266 TYR 0.019 0.001 TYR B 317 ARG 0.005 0.000 ARG B 385 ********************** 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 136 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.947 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: 0.9127 (t0) cc_final: 0.8577 (p0) REVERT: A 164 CYS cc_start: 0.8979 (m) cc_final: 0.8754 (p) REVERT: A 168 GLU cc_start: 0.7138 (tt0) cc_final: 0.6491 (tp30) REVERT: A 179 ASP cc_start: 0.8981 (t0) cc_final: 0.8608 (t0) REVERT: A 212 TYR cc_start: 0.8925 (p90) cc_final: 0.8674 (p90) REVERT: A 371 GLU cc_start: 0.9440 (tt0) cc_final: 0.9085 (pt0) REVERT: B 212 TYR cc_start: 0.9087 (t80) cc_final: 0.8686 (t80) REVERT: B 216 GLN cc_start: 0.9267 (mm110) cc_final: 0.8679 (mm110) REVERT: B 259 PHE cc_start: 0.9597 (t80) cc_final: 0.9209 (t80) REVERT: B 443 ARG cc_start: 0.9634 (ttp80) cc_final: 0.9416 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3872 time to fit residues: 67.8323 Evaluate side-chains 115 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 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: 2.3988 ------------------------------------------------------------------------------- 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.083144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065591 restraints weight = 77750.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.069138 restraints weight = 43688.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071789 restraints weight = 27996.700| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5795 Z= 0.246 Angle : 0.598 5.738 7813 Z= 0.356 Chirality : 0.038 0.159 871 Planarity : 0.005 0.059 1007 Dihedral : 5.342 25.235 786 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.02 % Favored : 87.69 % 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: -1.20 (0.30), residues: 707 helix: 0.32 (0.25), residues: 409 sheet: 0.20 (0.72), residues: 49 loop : -2.97 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 314 HIS 0.008 0.002 HIS B 426 PHE 0.020 0.002 PHE A 347 TYR 0.017 0.002 TYR B 317 ARG 0.005 0.001 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3001.28 seconds wall clock time: 53 minutes 17.71 seconds (3197.71 seconds total)