Starting phenix.real_space_refine on Wed Sep 25 20:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/09_2024/7rsi_24672_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/09_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_24672/09_2024/7rsi_24672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/09_2024/7rsi_24672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/09_2024/7rsi_24672_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsi_24672/09_2024/7rsi_24672_trim.cif" } 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. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10886 Number of models: 1 Model: "" Number of chains: 3 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: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4442 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} 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 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.04, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 764.1 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... Secondary structure from input PDB file: 31 helices and 3 sheets defined 63.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 5 through 22 Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.672A pdb=" N GLU B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.644A pdb=" N GLN B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 Processing helix chain 'B' and resid 201 through 221 removed outlier: 4.504A pdb=" N THR B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 Processing helix chain 'B' and resid 245 through 263 Processing helix chain 'B' and resid 265 through 280 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) Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 306 through 326 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 346 through 364 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 368 through 382 removed outlier: 4.205A pdb=" N LYS B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 411 removed outlier: 3.638A pdb=" N VAL B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 434 removed outlier: 3.524A pdb=" N ASP B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 455 through 460 Processing helix chain 'B' and resid 464 through 486 removed outlier: 3.545A pdb=" N TYR B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 93 through 102 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 118 through 124 Processing helix chain 'C' and resid 131 through 147 Processing helix chain 'C' and resid 199 through 213 Processing helix chain 'C' and resid 280 through 293 Processing helix chain 'C' and resid 311 through 316 Processing helix chain 'C' and resid 317 through 320 removed outlier: 3.877A pdb=" N LEU C 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 317 through 320' Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 353 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 80 removed outlier: 6.980A pdb=" N VAL C 14 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE C 80 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL C 16 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS C 13 " --> pdb=" O MET C 328 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA C 330 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 15 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL C 332 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG C 17 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS C 107 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE C 257 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 109 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'C' and resid 178 through 181 336 hydrogen bonds defined for protein. 993 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: 4.01 Time building geometry restraints manager: 3.82 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: 0.00 - 3.28: 18048 3.28 - 6.55: 1595 6.55 - 9.83: 100 9.83 - 13.10: 14 13.10 - 16.38: 6 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: 138 1.84 - 2.53: 9851 2.53 - 3.22: 35371 3.22 - 3.91: 43301 3.91 - 4.60: 67281 Nonbonded interactions: 155942 Sorted by model distance: nonbonded pdb=" O ARG B 21 " pdb="HH11 ARG B 21 " model vdw 1.154 2.450 nonbonded pdb=" OE1 GLU B 156 " pdb=" H GLU B 156 " model vdw 1.384 2.450 nonbonded pdb=" OE1 GLU B 225 " pdb=" H GLU B 225 " model vdw 1.415 2.450 nonbonded pdb=" OE1 GLU B 437 " pdb=" H GLU B 437 " model vdw 1.504 2.450 nonbonded pdb=" OG1 THR C 93 " pdb=" H THR C 94 " model vdw 1.513 2.450 ... (remaining 155937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- 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= 0.973 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 : 0.872 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: 0.4263 time to fit residues: 71.3207 Evaluate side-chains 103 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 B 330 GLN B 464 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5584 Z= 0.250 Angle : 0.707 6.949 7533 Z= 0.405 Chirality : 0.041 0.156 845 Planarity : 0.005 0.038 956 Dihedral : 11.023 170.051 752 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.82 % Favored : 95.03 % Rotamer: Outliers : 0.17 % Allowed : 1.21 % 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: -0.22 (0.32), residues: 664 helix: 0.24 (0.24), residues: 413 sheet: -0.79 (0.62), residues: 62 loop : -0.46 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.006 0.002 HIS B 105 PHE 0.018 0.002 PHE B 430 TYR 0.022 0.003 TYR B 317 ARG 0.005 0.001 ARG B 442 *********************** 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 124 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 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: symmetry clash revert: 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: 0.9450 (mmp) cc_final: 0.9175 (mmm) REVERT: B 329 MET cc_start: 0.9112 (tpp) cc_final: 0.8700 (mmm) REVERT: C 166 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7796 (tm-30) REVERT: C 176 PRO cc_start: 0.8566 (Cg_exo) cc_final: 0.8360 (Cg_endo) REVERT: C 236 LEU cc_start: 0.7483 (tp) cc_final: 0.6583 (tp) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.3992 time to fit residues: 62.3179 Evaluate side-chains 101 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 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: 0.7098 moved from start: 0.3262 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= 0.203 Angle : 0.604 6.550 7533 Z= 0.345 Chirality : 0.039 0.155 845 Planarity : 0.004 0.049 956 Dihedral : 10.391 166.124 752 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -0.16 (0.32), residues: 664 helix: 0.45 (0.25), residues: 414 sheet: -0.63 (0.67), residues: 62 loop : -0.95 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.007 0.001 HIS C 139 PHE 0.023 0.002 PHE C 76 TYR 0.017 0.002 TYR B 482 ARG 0.005 0.001 ARG B 450 *********************** 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 116 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.919 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: B 125 LEU cc_start: 0.8556 (mt) cc_final: 0.8350 (mt) REVERT: B 223 MET cc_start: 0.9422 (mmp) cc_final: 0.9184 (mmm) REVERT: C 166 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7835 (tm-30) REVERT: C 173 ASN cc_start: 0.7820 (t0) cc_final: 0.7580 (t0) REVERT: C 176 PRO cc_start: 0.8657 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: C 236 LEU cc_start: 0.6809 (tp) cc_final: 0.6476 (tp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.4105 time to fit residues: 60.4039 Evaluate side-chains 96 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 170 ASN B 209 HIS B 474 GLN C 211 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5584 Z= 0.177 Angle : 0.560 6.360 7533 Z= 0.317 Chirality : 0.038 0.150 845 Planarity : 0.004 0.050 956 Dihedral : 9.995 158.574 752 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -0.09 (0.32), residues: 664 helix: 0.60 (0.25), residues: 416 sheet: -0.82 (0.71), residues: 57 loop : -1.09 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 314 HIS 0.006 0.002 HIS B 209 PHE 0.014 0.002 PHE B 430 TYR 0.017 0.001 TYR B 169 ARG 0.003 0.000 ARG C 180 *********************** 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: 0 poor density : 112 time to evaluate : 0.820 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: B 139 ILE cc_start: 0.9743 (pt) cc_final: 0.9461 (pt) REVERT: B 142 GLN cc_start: 0.9446 (mt0) cc_final: 0.9148 (mt0) REVERT: B 223 MET cc_start: 0.9398 (mmp) cc_final: 0.9162 (mmm) REVERT: B 263 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8839 (mmtt) REVERT: B 481 TYR cc_start: 0.6960 (m-10) cc_final: 0.6522 (m-10) REVERT: C 166 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7809 (tm-30) REVERT: C 176 PRO cc_start: 0.8649 (Cg_exo) cc_final: 0.8414 (Cg_endo) REVERT: C 232 PHE cc_start: 0.9493 (m-80) cc_final: 0.8901 (m-80) REVERT: C 236 LEU cc_start: 0.6910 (tp) cc_final: 0.6508 (tp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3872 time to fit residues: 55.7594 Evaluate side-chains 97 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 170 ASN ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4067 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= 0.174 Angle : 0.543 6.399 7533 Z= 0.306 Chirality : 0.037 0.152 845 Planarity : 0.004 0.047 956 Dihedral : 9.001 129.138 752 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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: -0.06 (0.32), residues: 664 helix: 0.67 (0.25), residues: 419 sheet: -0.85 (0.70), residues: 57 loop : -1.22 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 6 HIS 0.007 0.002 HIS B 401 PHE 0.010 0.002 PHE B 203 TYR 0.017 0.001 TYR B 169 ARG 0.002 0.000 ARG B 40 *********************** 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 109 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.796 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 139 ILE cc_start: 0.9727 (pt) cc_final: 0.9423 (pt) REVERT: B 142 GLN cc_start: 0.9427 (mt0) cc_final: 0.9131 (mt0) REVERT: B 223 MET cc_start: 0.9388 (mmp) cc_final: 0.9165 (mmm) REVERT: B 481 TYR cc_start: 0.6939 (m-10) cc_final: 0.6555 (m-10) REVERT: C 107 CYS cc_start: 0.7489 (t) cc_final: 0.7071 (t) REVERT: C 166 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7905 (tm-30) REVERT: C 176 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8455 (Cg_endo) REVERT: C 231 VAL cc_start: 0.8649 (t) cc_final: 0.8428 (t) REVERT: C 232 PHE cc_start: 0.9447 (m-80) cc_final: 0.8880 (m-80) REVERT: C 236 LEU cc_start: 0.7015 (tp) cc_final: 0.6630 (tp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3999 time to fit residues: 55.9158 Evaluate side-chains 98 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 8.9990 chunk 16 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5584 Z= 0.160 Angle : 0.534 6.074 7533 Z= 0.299 Chirality : 0.037 0.137 845 Planarity : 0.004 0.048 956 Dihedral : 8.728 123.991 752 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % 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: 0.00 (0.32), residues: 664 helix: 0.74 (0.25), residues: 419 sheet: -0.81 (0.69), residues: 57 loop : -1.27 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 6 HIS 0.010 0.002 HIS B 100 PHE 0.024 0.002 PHE B 430 TYR 0.016 0.001 TYR B 169 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 111 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.794 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 139 ILE cc_start: 0.9729 (pt) cc_final: 0.9430 (pt) REVERT: B 142 GLN cc_start: 0.9409 (mt0) cc_final: 0.9112 (mt0) REVERT: B 223 MET cc_start: 0.9366 (mmp) cc_final: 0.9116 (mmm) REVERT: B 318 CYS cc_start: 0.9517 (m) cc_final: 0.9303 (p) REVERT: B 426 HIS cc_start: 0.9375 (t-170) cc_final: 0.9056 (t-90) REVERT: B 481 TYR cc_start: 0.6146 (m-10) cc_final: 0.5884 (m-10) REVERT: C 176 PRO cc_start: 0.8680 (Cg_exo) cc_final: 0.8439 (Cg_endo) REVERT: C 231 VAL cc_start: 0.8634 (t) cc_final: 0.8428 (t) REVERT: C 232 PHE cc_start: 0.9372 (m-80) cc_final: 0.8825 (m-80) REVERT: C 236 LEU cc_start: 0.7115 (tp) cc_final: 0.6731 (tp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3998 time to fit residues: 56.7327 Evaluate side-chains 95 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5584 Z= 0.158 Angle : 0.522 6.016 7533 Z= 0.292 Chirality : 0.037 0.137 845 Planarity : 0.004 0.048 956 Dihedral : 8.166 110.183 752 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: 0.16 (0.33), residues: 664 helix: 0.95 (0.26), residues: 417 sheet: -1.16 (0.65), residues: 62 loop : -1.25 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 6 HIS 0.007 0.001 HIS B 100 PHE 0.015 0.001 PHE B 430 TYR 0.015 0.001 TYR B 169 ARG 0.003 0.000 ARG B 270 *********************** 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 108 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.842 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 426 HIS cc_start: 0.9294 (t-170) cc_final: 0.8992 (t-90) REVERT: B 481 TYR cc_start: 0.6138 (m-10) cc_final: 0.5838 (m-10) REVERT: C 231 VAL cc_start: 0.8651 (t) cc_final: 0.8421 (t) REVERT: C 232 PHE cc_start: 0.9358 (m-80) cc_final: 0.8652 (m-80) REVERT: C 236 LEU cc_start: 0.7165 (tp) cc_final: 0.6796 (tp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3991 time to fit residues: 55.2703 Evaluate side-chains 95 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5584 Z= 0.162 Angle : 0.522 6.356 7533 Z= 0.290 Chirality : 0.037 0.134 845 Planarity : 0.004 0.049 956 Dihedral : 7.617 95.854 752 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: 0.13 (0.32), residues: 664 helix: 0.96 (0.26), residues: 420 sheet: -1.18 (0.65), residues: 62 loop : -1.37 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 6 HIS 0.008 0.001 HIS B 426 PHE 0.017 0.001 PHE B 430 TYR 0.015 0.001 TYR B 169 ARG 0.002 0.000 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 106 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.923 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 223 MET cc_start: 0.9312 (mmp) cc_final: 0.9028 (mmm) REVERT: B 481 TYR cc_start: 0.6183 (m-10) cc_final: 0.5866 (m-10) REVERT: C 147 ILE cc_start: 0.8749 (pt) cc_final: 0.8443 (pt) REVERT: C 232 PHE cc_start: 0.9372 (m-80) cc_final: 0.8691 (m-80) REVERT: C 236 LEU cc_start: 0.7158 (tp) cc_final: 0.6597 (tp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.4044 time to fit residues: 54.8043 Evaluate side-chains 95 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 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 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5584 Z= 0.172 Angle : 0.533 6.046 7533 Z= 0.300 Chirality : 0.037 0.135 845 Planarity : 0.004 0.048 956 Dihedral : 6.690 86.823 752 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: 0.11 (0.33), residues: 664 helix: 0.94 (0.26), residues: 419 sheet: -1.16 (0.66), residues: 59 loop : -1.38 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 6 HIS 0.018 0.002 HIS B 426 PHE 0.039 0.002 PHE B 430 TYR 0.021 0.001 TYR B 317 ARG 0.002 0.000 ARG B 126 *********************** 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 106 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.873 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: B 481 TYR cc_start: 0.6175 (m-10) cc_final: 0.5853 (m-10) REVERT: C 232 PHE cc_start: 0.9352 (m-80) cc_final: 0.8850 (m-80) REVERT: C 236 LEU cc_start: 0.7130 (tp) cc_final: 0.6765 (tp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.4043 time to fit residues: 54.5607 Evaluate side-chains 92 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5584 Z= 0.168 Angle : 0.518 6.164 7533 Z= 0.291 Chirality : 0.037 0.135 845 Planarity : 0.004 0.049 956 Dihedral : 6.601 82.901 752 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: 0.19 (0.33), residues: 664 helix: 1.00 (0.26), residues: 419 sheet: -0.95 (0.68), residues: 57 loop : -1.41 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 6 HIS 0.006 0.001 HIS B 232 PHE 0.029 0.002 PHE B 430 TYR 0.019 0.001 TYR B 317 ARG 0.003 0.000 ARG B 443 ********************** 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 106 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.948 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: B 223 MET cc_start: 0.9293 (mmp) cc_final: 0.9016 (mmm) REVERT: B 481 TYR cc_start: 0.6178 (m-10) cc_final: 0.5694 (m-10) REVERT: C 232 PHE cc_start: 0.9349 (m-80) cc_final: 0.8917 (m-80) REVERT: C 236 LEU cc_start: 0.7107 (tp) cc_final: 0.6620 (tp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.4046 time to fit residues: 54.6456 Evaluate side-chains 91 residues out of total 599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 7.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.075553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057307 restraints weight = 113374.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059786 restraints weight = 74105.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061678 restraints weight = 52807.881| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5584 Z= 0.238 Angle : 0.592 6.308 7533 Z= 0.337 Chirality : 0.038 0.147 845 Planarity : 0.004 0.049 956 Dihedral : 6.766 85.937 752 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.61 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: -0.09 (0.33), residues: 664 helix: 0.72 (0.26), residues: 417 sheet: -0.76 (0.71), residues: 55 loop : -1.44 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 6 HIS 0.008 0.002 HIS B 419 PHE 0.028 0.002 PHE B 430 TYR 0.022 0.002 TYR B 317 ARG 0.006 0.001 ARG B 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.99 seconds wall clock time: 53 minutes 23.81 seconds (3203.81 seconds total)