Starting phenix.real_space_refine on Fri Mar 15 06:31:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/03_2024/7rsi_24672_trim_updated.pdb" } resolution = 4.9 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= 0.013 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 31 5.16 5 C 3472 2.51 5 N 953 2.21 5 O 1027 1.98 5 H 5400 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 244": "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 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 365": "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 PHE 430": "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 "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 339": "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: 10886 Number of models: 1 Model: "" Number of chains: 2 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 Chain: "C" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4470 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 294, 'undetermined': 2} Link IDs: {'PTRANS': 6, 'TRANS': 287, None: 2} Not linked: pdbres="LYS C 353 " pdbres=" MG C 501 " Not linked: pdbres=" MG C 501 " pdbres="ADP C 502 " Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 5.16, per 1000 atoms: 0.47 Number of scatterers: 10886 At special positions: 0 Unit cell: (64.61, 97.37, 111.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 31 16.00 P 2 15.00 Mg 1 11.99 O 1027 8.00 N 953 7.00 C 3472 6.00 H 5400 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: 9.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 3 sheets defined 56.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 39 through 51 Processing helix chain 'B' and resid 87 through 104 Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 202 through 220 removed outlier: 4.504A pdb=" N THR B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 Processing helix chain 'B' and resid 246 through 262 Processing helix chain 'B' and resid 266 through 281 removed outlier: 4.925A pdb=" N HIS B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N CYS B 272 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 328 removed outlier: 6.066A pdb=" N LYS B 307 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 363 removed outlier: 4.284A pdb=" N ARG B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 removed outlier: 4.205A pdb=" N LYS B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 410 removed outlier: 3.638A pdb=" N VAL B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 433 removed outlier: 3.553A pdb=" N VAL B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 465 through 485 removed outlier: 3.545A pdb=" N TYR B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 94 through 101 removed outlier: 3.598A pdb=" N ARG C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER C 100 " --> pdb=" O PRO C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 132 through 146 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 336 through 352 removed outlier: 5.387A pdb=" N ASP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 78 through 80 removed outlier: 3.997A pdb=" N ALA C 78 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN C 106 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE C 327 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR C 108 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 329 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU C 110 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA C 331 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR C 112 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'C' and resid 178 through 181 309 hydrogen bonds defined for protein. 792 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: 3.67 Time building geometry restraints manager: 9.66 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: 5386 1.13 - 1.30: 918 1.30 - 1.47: 2206 1.47 - 1.64: 2426 1.64 - 1.81: 48 Bond restraints: 10984 Sorted by residual: bond pdb=" CZ3 TRP B 314 " pdb=" HZ3 TRP B 314 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" CD2 PHE B 409 " pdb=" HD2 PHE B 409 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" CE1 TYR B 230 " pdb=" HE1 TYR B 230 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" N VAL C 187 " pdb=" H VAL C 187 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" CD2 PHE B 203 " pdb=" HD2 PHE B 203 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 10979 not shown) Histogram of bond angle deviations from ideal: 95.04 - 103.00: 34 103.00 - 110.96: 11758 110.96 - 118.92: 3010 118.92 - 126.87: 4871 126.87 - 134.83: 90 Bond angle restraints: 19763 Sorted by residual: angle pdb=" N ASP B 339 " pdb=" CA ASP B 339 " pdb=" C ASP B 339 " ideal model delta sigma weight residual 111.69 99.23 12.46 1.23e+00 6.61e-01 1.03e+02 angle pdb=" C GLN C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.52 129.44 -8.92 9.90e-01 1.02e+00 8.12e+01 angle pdb=" C SER C 333 " pdb=" N PRO C 334 " pdb=" CA PRO C 334 " ideal model delta sigma weight residual 119.64 128.12 -8.48 1.01e+00 9.80e-01 7.05e+01 angle pdb=" C GLY B 51 " pdb=" N PRO B 52 " pdb=" CA PRO B 52 " ideal model delta sigma weight residual 119.47 129.14 -9.67 1.16e+00 7.43e-01 6.95e+01 angle pdb=" C GLY C 175 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " ideal model delta sigma weight residual 119.93 128.84 -8.91 1.07e+00 8.73e-01 6.94e+01 ... (remaining 19758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.00: 5039 33.00 - 66.00: 87 66.00 - 98.99: 5 98.99 - 131.99: 1 131.99 - 164.99: 2 Dihedral angle restraints: 5134 sinusoidal: 2746 harmonic: 2388 Sorted by residual: dihedral pdb=" O1B ADP C 502 " pdb=" O3A ADP C 502 " pdb=" PB ADP C 502 " pdb=" PA ADP C 502 " ideal model delta sinusoidal sigma weight residual -60.00 104.98 -164.99 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP C 502 " pdb=" O5' ADP C 502 " pdb=" PA ADP C 502 " pdb=" O2A ADP C 502 " ideal model delta sinusoidal sigma weight residual -60.00 101.71 -161.70 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP C 502 " pdb=" O3A ADP C 502 " pdb=" PA ADP C 502 " pdb=" PB ADP C 502 " ideal model delta sinusoidal sigma weight residual -60.00 56.76 -116.76 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 485 0.055 - 0.109: 252 0.109 - 0.163: 85 0.163 - 0.218: 19 0.218 - 0.272: 4 Chirality restraints: 845 Sorted by residual: chirality pdb=" CA ARG B 126 " pdb=" N ARG B 126 " pdb=" C ARG B 126 " pdb=" CB ARG B 126 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TYR B 218 " pdb=" N TYR B 218 " pdb=" C TYR B 218 " pdb=" CB TYR B 218 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN B 242 " pdb=" N ASN B 242 " pdb=" C ASN B 242 " pdb=" CB ASN B 242 " 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 842 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 502 " -0.468 2.00e-02 2.50e+03 1.84e-01 9.35e+02 pdb=" C2 ADP C 502 " 0.056 2.00e-02 2.50e+03 pdb=" C4 ADP C 502 " 0.128 2.00e-02 2.50e+03 pdb=" C5 ADP C 502 " 0.025 2.00e-02 2.50e+03 pdb=" C6 ADP C 502 " -0.071 2.00e-02 2.50e+03 pdb=" C8 ADP C 502 " 0.175 2.00e-02 2.50e+03 pdb=" N1 ADP C 502 " -0.046 2.00e-02 2.50e+03 pdb=" N3 ADP C 502 " 0.139 2.00e-02 2.50e+03 pdb=" N6 ADP C 502 " -0.193 2.00e-02 2.50e+03 pdb=" N7 ADP C 502 " 0.066 2.00e-02 2.50e+03 pdb=" N9 ADP C 502 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 271 " 0.078 2.00e-02 2.50e+03 7.91e-02 1.41e+02 pdb=" CG HIS B 271 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 271 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS B 271 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 271 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS B 271 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 HIS B 271 " -0.183 2.00e-02 2.50e+03 pdb=" HD2 HIS B 271 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS B 271 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 31 " 0.066 2.00e-02 2.50e+03 7.67e-02 1.32e+02 pdb=" CG HIS C 31 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS C 31 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 HIS C 31 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS C 31 " 0.038 2.00e-02 2.50e+03 pdb=" NE2 HIS C 31 " -0.021 2.00e-02 2.50e+03 pdb=" HD1 HIS C 31 " -0.178 2.00e-02 2.50e+03 pdb=" HD2 HIS C 31 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS C 31 " 0.053 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 146 1.84 - 2.53: 9897 2.53 - 3.22: 35377 3.22 - 3.91: 43321 3.91 - 4.60: 67336 Nonbonded interactions: 156077 Sorted by model distance: nonbonded pdb=" O ARG B 21 " pdb="HH11 ARG B 21 " model vdw 1.154 1.850 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.384 1.850 nonbonded pdb=" OE1 GLU B 225 " pdb=" H GLU B 225 " model vdw 1.415 1.850 nonbonded pdb=" OE1 GLU B 437 " pdb=" H GLU B 437 " model vdw 1.504 1.850 nonbonded pdb=" OG1 THR C 93 " pdb=" H THR C 94 " model vdw 1.513 1.850 ... (remaining 156072 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: 1.280 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: 0.180 Extract box with map and model: 6.190 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.740 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 0.102 5584 Z= 0.972 Angle : 1.512 16.376 7533 Z= 1.030 Chirality : 0.073 0.272 845 Planarity : 0.009 0.184 956 Dihedral : 12.443 164.987 2054 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.52 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.32 (0.31), residues: 664 helix: 0.01 (0.23), residues: 398 sheet: -1.10 (0.64), residues: 49 loop : -0.06 (0.47), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.007 TRP B 314 HIS 0.007 0.002 HIS C 229 PHE 0.030 0.006 PHE B 280 TYR 0.068 0.008 TYR B 482 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.940 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: B 223 MET cc_start: 0.9538 (mmp) cc_final: 0.9319 (mmm) REVERT: C 166 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7877 (tm-30) REVERT: C 173 ASN cc_start: 0.7473 (t0) cc_final: 0.7209 (t0) REVERT: C 176 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: C 236 LEU cc_start: 0.7363 (tp) cc_final: 0.7093 (tp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4145 time to fit residues: 69.1788 Evaluate side-chains 103 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS B 209 HIS B 324 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5584 Z= 0.209 Angle : 0.649 7.074 7533 Z= 0.373 Chirality : 0.040 0.160 845 Planarity : 0.005 0.037 956 Dihedral : 10.951 161.146 752 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.24 (0.32), residues: 664 helix: 0.24 (0.25), residues: 397 sheet: -0.81 (0.60), residues: 62 loop : -0.44 (0.48), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.007 0.001 HIS C 139 PHE 0.018 0.002 PHE B 430 TYR 0.023 0.002 TYR B 317 ARG 0.006 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.897 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: B 223 MET cc_start: 0.9443 (mmp) cc_final: 0.9187 (mmm) REVERT: B 453 MET cc_start: 0.3025 (mmp) cc_final: 0.2520 (ttp) REVERT: C 166 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7831 (tm-30) REVERT: C 236 LEU cc_start: 0.7464 (tp) cc_final: 0.6317 (tp) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.3961 time to fit residues: 63.0167 Evaluate side-chains 102 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5584 Z= 0.271 Angle : 0.685 8.157 7533 Z= 0.396 Chirality : 0.040 0.160 845 Planarity : 0.005 0.051 956 Dihedral : 10.200 150.927 752 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.23 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.76 (0.32), residues: 664 helix: -0.05 (0.25), residues: 403 sheet: -0.83 (0.62), residues: 62 loop : -1.06 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 249 HIS 0.009 0.002 HIS B 447 PHE 0.021 0.002 PHE B 430 TYR 0.021 0.002 TYR B 383 ARG 0.006 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.943 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: B 223 MET cc_start: 0.9447 (mmp) cc_final: 0.9233 (mmm) REVERT: B 453 MET cc_start: 0.3503 (mmp) cc_final: 0.2594 (ttp) REVERT: C 236 LEU cc_start: 0.6865 (tp) cc_final: 0.6486 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.4345 time to fit residues: 58.9058 Evaluate side-chains 88 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5584 Z= 0.144 Angle : 0.532 6.022 7533 Z= 0.298 Chirality : 0.038 0.148 845 Planarity : 0.004 0.050 956 Dihedral : 9.597 140.380 752 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 664 helix: 0.23 (0.25), residues: 403 sheet: -0.62 (0.68), residues: 57 loop : -0.85 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 314 HIS 0.008 0.001 HIS B 209 PHE 0.016 0.002 PHE B 396 TYR 0.017 0.002 TYR B 317 ARG 0.003 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.886 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: B 125 LEU cc_start: 0.8751 (mt) cc_final: 0.8524 (mt) REVERT: B 329 MET cc_start: 0.9223 (tpp) cc_final: 0.8643 (tpp) REVERT: B 331 ASP cc_start: 0.9427 (m-30) cc_final: 0.9159 (m-30) REVERT: C 236 LEU cc_start: 0.6969 (tp) cc_final: 0.6591 (tp) outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.3974 time to fit residues: 56.8589 Evaluate side-chains 97 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5584 Z= 0.240 Angle : 0.613 6.350 7533 Z= 0.354 Chirality : 0.038 0.142 845 Planarity : 0.004 0.050 956 Dihedral : 8.950 128.831 752 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.66 (0.32), residues: 664 helix: 0.04 (0.25), residues: 402 sheet: -0.75 (0.69), residues: 57 loop : -1.04 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 249 HIS 0.008 0.001 HIS B 401 PHE 0.016 0.002 PHE B 430 TYR 0.018 0.002 TYR B 169 ARG 0.006 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.978 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: B 223 MET cc_start: 0.9379 (mmp) cc_final: 0.9156 (mmm) REVERT: B 329 MET cc_start: 0.9215 (tpp) cc_final: 0.8639 (tpp) REVERT: B 331 ASP cc_start: 0.9434 (m-30) cc_final: 0.9165 (m-30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4032 time to fit residues: 53.7176 Evaluate side-chains 87 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5584 Z= 0.158 Angle : 0.532 6.163 7533 Z= 0.298 Chirality : 0.037 0.144 845 Planarity : 0.004 0.050 956 Dihedral : 8.556 134.350 752 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.44 (0.32), residues: 664 helix: 0.25 (0.25), residues: 398 sheet: -0.74 (0.69), residues: 57 loop : -1.01 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 314 HIS 0.009 0.001 HIS B 100 PHE 0.024 0.002 PHE B 13 TYR 0.016 0.001 TYR B 317 ARG 0.002 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 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: B 329 MET cc_start: 0.9222 (tpp) cc_final: 0.8651 (tpp) REVERT: B 331 ASP cc_start: 0.9430 (m-30) cc_final: 0.9160 (m-30) REVERT: C 232 PHE cc_start: 0.8862 (m-80) cc_final: 0.8400 (m-80) REVERT: C 338 PHE cc_start: 0.7700 (m-80) cc_final: 0.7499 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3767 time to fit residues: 51.7054 Evaluate side-chains 91 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5584 Z= 0.173 Angle : 0.548 6.564 7533 Z= 0.306 Chirality : 0.037 0.139 845 Planarity : 0.004 0.049 956 Dihedral : 8.269 141.969 752 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.43 (0.32), residues: 664 helix: 0.32 (0.25), residues: 400 sheet: -0.99 (0.67), residues: 62 loop : -1.07 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 249 HIS 0.006 0.001 HIS B 100 PHE 0.016 0.002 PHE B 13 TYR 0.017 0.001 TYR B 317 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.931 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: B 329 MET cc_start: 0.9179 (tpp) cc_final: 0.8566 (tpp) REVERT: B 331 ASP cc_start: 0.9439 (m-30) cc_final: 0.9166 (m-30) REVERT: C 232 PHE cc_start: 0.8858 (m-80) cc_final: 0.8404 (m-80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4017 time to fit residues: 53.8340 Evaluate side-chains 90 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5584 Z= 0.273 Angle : 0.666 7.195 7533 Z= 0.382 Chirality : 0.039 0.181 845 Planarity : 0.005 0.057 956 Dihedral : 8.756 160.610 752 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.32), residues: 664 helix: -0.12 (0.25), residues: 393 sheet: -1.25 (0.64), residues: 62 loop : -1.02 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 249 HIS 0.007 0.002 HIS B 419 PHE 0.022 0.002 PHE B 389 TYR 0.020 0.002 TYR B 169 ARG 0.005 0.001 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.973 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: B 329 MET cc_start: 0.9170 (tpp) cc_final: 0.8553 (tpp) REVERT: B 331 ASP cc_start: 0.9424 (m-30) cc_final: 0.9158 (m-30) REVERT: C 232 PHE cc_start: 0.8849 (m-80) cc_final: 0.8340 (m-80) REVERT: C 236 LEU cc_start: 0.7292 (tp) cc_final: 0.6804 (tp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3922 time to fit residues: 48.3926 Evaluate side-chains 82 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 0.0270 chunk 40 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5584 Z= 0.144 Angle : 0.527 5.915 7533 Z= 0.292 Chirality : 0.037 0.140 845 Planarity : 0.004 0.052 956 Dihedral : 8.675 164.718 752 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.36 (0.33), residues: 664 helix: 0.31 (0.26), residues: 397 sheet: -1.00 (0.66), residues: 62 loop : -0.83 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 249 HIS 0.009 0.001 HIS B 426 PHE 0.023 0.002 PHE B 430 TYR 0.016 0.002 TYR B 317 ARG 0.006 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.955 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: B 329 MET cc_start: 0.9128 (tpp) cc_final: 0.8539 (tpp) REVERT: B 331 ASP cc_start: 0.9420 (m-30) cc_final: 0.9142 (m-30) REVERT: C 232 PHE cc_start: 0.8860 (m-80) cc_final: 0.8413 (m-80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3689 time to fit residues: 48.9643 Evaluate side-chains 87 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5584 Z= 0.157 Angle : 0.534 5.687 7533 Z= 0.299 Chirality : 0.037 0.135 845 Planarity : 0.004 0.051 956 Dihedral : 8.695 171.621 752 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.32 (0.33), residues: 664 helix: 0.36 (0.26), residues: 400 sheet: -0.93 (0.67), residues: 62 loop : -0.92 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 314 HIS 0.006 0.001 HIS B 232 PHE 0.020 0.002 PHE B 430 TYR 0.022 0.002 TYR B 317 ARG 0.003 0.000 ARG B 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 276 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue ILE 281 is missing expected H atoms. Skipping. Residue SER 284 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue LEU 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue VAL 291 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 295 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.972 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: B 329 MET cc_start: 0.9127 (tpp) cc_final: 0.8516 (tpp) REVERT: B 331 ASP cc_start: 0.9434 (m-30) cc_final: 0.9164 (m-30) REVERT: C 232 PHE cc_start: 0.8830 (m-80) cc_final: 0.8447 (m-80) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.3844 time to fit residues: 49.5665 Evaluate side-chains 86 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0000 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.078499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058123 restraints weight = 109212.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060926 restraints weight = 70616.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.063062 restraints weight = 49515.676| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5584 Z= 0.148 Angle : 0.515 5.734 7533 Z= 0.287 Chirality : 0.036 0.131 845 Planarity : 0.004 0.051 956 Dihedral : 8.798 178.616 752 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.14 (0.33), residues: 664 helix: 0.53 (0.26), residues: 396 sheet: -0.91 (0.67), residues: 62 loop : -0.84 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 149 HIS 0.007 0.001 HIS B 426 PHE 0.022 0.001 PHE B 430 TYR 0.023 0.002 TYR B 317 ARG 0.003 0.000 ARG B 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.40 seconds wall clock time: 54 minutes 8.97 seconds (3248.97 seconds total)