Starting phenix.real_space_refine (version: dev) on Mon Dec 12 15:10:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/12_2022/7rsi_24672_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/12_2022/7rsi_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_24672/12_2022/7rsi_24672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/12_2022/7rsi_24672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/12_2022/7rsi_24672_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/12_2022/7rsi_24672_trim_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.40, per 1000 atoms: 0.50 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: 9.69 Conformation dependent library (CDL) restraints added in 936.0 milliseconds 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: 0.73 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: 3.88 Time building geometry restraints manager: 9.97 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: 4373 33.00 - 66.00: 49 66.00 - 98.99: 5 98.99 - 131.99: 1 131.99 - 164.99: 2 Dihedral angle restraints: 4430 sinusoidal: 2042 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 4427 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 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. 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: 1.010 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: 0.170 Extract box with map and model: 6.490 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 38.950 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 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 : 6.36 Ramachandran Plot: Outliers : 0.90 % Allowed : 4.52 % Favored : 94.58 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.957 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 outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.4004 time to fit residues: 67.8982 Evaluate side-chains 100 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0803 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 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: 0.6815 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5584 Z= 0.218 Angle : 0.653 7.212 7533 Z= 0.374 Chirality : 0.040 0.157 845 Planarity : 0.005 0.037 956 Dihedral : 10.997 161.400 752 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.52 % Favored : 95.33 % Rotamer Outliers : 0.17 % 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 (0.33), residues: 664 helix: 0.23 (0.25), residues: 397 sheet: -0.80 (0.60), residues: 62 loop : -0.41 (0.49), residues: 205 *********************** 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 123 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.912 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 outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.3710 time to fit residues: 58.1864 Evaluate side-chains 101 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1564 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN B 464 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 5584 Z= 0.252 Angle : 0.667 7.753 7533 Z= 0.384 Chirality : 0.039 0.151 845 Planarity : 0.005 0.050 956 Dihedral : 10.216 150.863 752 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer Outliers : 0.00 % 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: -0.70 (0.32), residues: 664 helix: -0.05 (0.25), residues: 406 sheet: -0.79 (0.61), residues: 62 loop : -0.95 (0.46), residues: 196 *********************** 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 109 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.898 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3977 time to fit residues: 55.4029 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1801 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5584 Z= 0.206 Angle : 0.592 7.048 7533 Z= 0.338 Chirality : 0.038 0.148 845 Planarity : 0.004 0.051 956 Dihedral : 9.711 138.275 752 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.17 % 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: -0.06 (0.25), residues: 406 sheet: -0.85 (0.67), residues: 57 loop : -1.04 (0.44), residues: 201 *********************** 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 109 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.812 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 outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.3579 time to fit residues: 51.0460 Evaluate side-chains 93 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1676 time to fit residues: 1.3075 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.6927 moved from start: 0.4131 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= 0.191 Angle : 0.569 5.900 7533 Z= 0.324 Chirality : 0.037 0.145 845 Planarity : 0.004 0.050 956 Dihedral : 8.934 131.315 752 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.00 % 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: -0.60 (0.32), residues: 664 helix: 0.10 (0.25), residues: 404 sheet: -0.73 (0.70), residues: 57 loop : -1.06 (0.44), residues: 203 *********************** 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 106 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.939 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 outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3709 time to fit residues: 51.2015 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1759 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 474 GLN ** 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: 0.6966 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 5584 Z= 0.230 Angle : 0.608 7.603 7533 Z= 0.346 Chirality : 0.037 0.145 845 Planarity : 0.004 0.052 956 Dihedral : 8.683 134.479 752 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.00 % 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: -0.82 (0.32), residues: 664 helix: -0.05 (0.25), residues: 397 sheet: -1.18 (0.64), residues: 62 loop : -1.06 (0.44), residues: 205 *********************** 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 105 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.927 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 outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3596 time to fit residues: 49.4540 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1268 ------------------------------------------------------------------------------- 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: 0.4980 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 474 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: 0.6927 moved from start: 0.4518 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= 0.166 Angle : 0.556 7.081 7533 Z= 0.309 Chirality : 0.037 0.144 845 Planarity : 0.004 0.051 956 Dihedral : 8.421 139.672 752 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.00 % 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: -0.67 (0.32), residues: 664 helix: 0.09 (0.25), residues: 402 sheet: -1.10 (0.65), residues: 62 loop : -1.05 (0.44), residues: 200 *********************** 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 107 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 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 outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3636 time to fit residues: 50.9372 Evaluate side-chains 88 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3113 ------------------------------------------------------------------------------- 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: 8.9990 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** 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: 0.6998 moved from start: 0.4810 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= 0.225 Angle : 0.604 6.090 7533 Z= 0.344 Chirality : 0.038 0.148 845 Planarity : 0.004 0.052 956 Dihedral : 8.561 154.692 752 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.00 % 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: -0.83 (0.32), residues: 664 helix: -0.05 (0.25), residues: 398 sheet: -1.21 (0.64), residues: 62 loop : -1.06 (0.44), residues: 204 *********************** 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 104 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.964 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 outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3650 time to fit residues: 49.7127 Evaluate side-chains 86 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1756 ------------------------------------------------------------------------------- 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: 0.5980 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 474 GLN ** 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: 0.6949 moved from start: 0.4914 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= 0.164 Angle : 0.544 5.711 7533 Z= 0.304 Chirality : 0.037 0.138 845 Planarity : 0.004 0.052 956 Dihedral : 8.623 162.142 752 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.00 % 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: -0.52 (0.32), residues: 664 helix: 0.22 (0.26), residues: 396 sheet: -1.13 (0.65), residues: 62 loop : -0.96 (0.44), residues: 206 *********************** 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 103 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.986 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 outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3723 time to fit residues: 50.7552 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4772 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.6948 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 5584 Z= 0.156 Angle : 0.524 5.679 7533 Z= 0.293 Chirality : 0.037 0.133 845 Planarity : 0.004 0.051 956 Dihedral : 8.643 169.896 752 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.00 % 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: -0.39 (0.32), residues: 664 helix: 0.37 (0.26), residues: 399 sheet: -1.09 (0.65), residues: 62 loop : -1.02 (0.44), residues: 203 ********************** 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 102 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.878 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 outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3703 time to fit residues: 48.9523 Evaluate side-chains 89 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0898 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.078277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056133 restraints weight = 114872.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.059150 restraints weight = 71170.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.061513 restraints weight = 48365.431| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4989 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 5584 Z= 0.140 Angle : 0.506 5.653 7533 Z= 0.279 Chirality : 0.036 0.133 845 Planarity : 0.004 0.051 956 Dihedral : 8.680 175.254 752 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.00 % 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: -0.11 (0.33), residues: 664 helix: 0.65 (0.26), residues: 392 sheet: -0.88 (0.66), residues: 62 loop : -1.03 (0.43), residues: 210 =============================================================================== Job complete usr+sys time: 2870.47 seconds wall clock time: 51 minutes 20.59 seconds (3080.59 seconds total)