Starting phenix.real_space_refine on Tue Jul 29 07:40:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_24672_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_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/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_24672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_24672.map" model { file = "/net/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_24672_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsi_24672/07_2025/7rsi_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-5711/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: 5.69, per 1000 atoms: 0.52 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: 3.17 Conformation dependent library (CDL) restraints added in 751.2 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: 0.87 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: 3.65 Time building geometry restraints manager: 3.79 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: 1.940 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: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.760 Find NCS groups from input model: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- 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= 0.948 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 Details of bonding type rmsd hydrogen bonds : bond 0.17460 ( 336) hydrogen bonds : angle 7.56430 ( 993) covalent geometry : bond 0.01489 ( 5584) covalent geometry : angle 1.51234 ( 7533) *********************** 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 to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.823 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: 0.4574 time to fit residues: 77.0231 Evaluate side-chains 103 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.079456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.056955 restraints weight = 102018.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060371 restraints weight = 60520.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063011 restraints weight = 40007.551| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5213 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= 0.224 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 Details of bonding type rmsd hydrogen bonds : bond 0.07127 ( 336) hydrogen bonds : angle 6.27556 ( 993) covalent geometry : bond 0.00394 ( 5584) covalent geometry : angle 0.70687 ( 7533) *********************** 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 to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.854 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 125 LEU cc_start: 0.7756 (mt) cc_final: 0.7548 (mt) REVERT: C 166 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7633 (tm-30) REVERT: C 236 LEU cc_start: 0.7908 (tp) cc_final: 0.7120 (tp) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.4073 time to fit residues: 63.9030 Evaluate side-chains 100 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN C 211 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.076036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.054651 restraints weight = 107465.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057824 restraints weight = 62812.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060273 restraints weight = 41031.622| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5300 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5584 Z= 0.331 Angle : 0.786 9.336 7533 Z= 0.455 Chirality : 0.042 0.192 845 Planarity : 0.006 0.054 956 Dihedral : 10.930 174.777 752 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.68 % Favored : 92.17 % Rotamer: Outliers : 0.17 % Allowed : 2.60 % Favored : 97.23 % 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: -1.14 (0.31), residues: 664 helix: -0.31 (0.24), residues: 411 sheet: -1.00 (0.65), residues: 62 loop : -1.33 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 314 HIS 0.009 0.002 HIS B 447 PHE 0.026 0.003 PHE C 76 TYR 0.026 0.003 TYR B 482 ARG 0.007 0.001 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.06852 ( 336) hydrogen bonds : angle 6.47402 ( 993) covalent geometry : bond 0.00565 ( 5584) covalent geometry : angle 0.78579 ( 7533) *********************** 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 103 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.928 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: C 173 ASN cc_start: 0.7889 (t0) cc_final: 0.7682 (t0) REVERT: C 236 LEU cc_start: 0.7478 (tp) cc_final: 0.7276 (tp) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.4457 time to fit residues: 57.8013 Evaluate side-chains 83 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 209 HIS ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.077262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059455 restraints weight = 110282.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.061948 restraints weight = 72127.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.063783 restraints weight = 51050.180| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3966 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= 0.138 Angle : 0.561 6.178 7533 Z= 0.314 Chirality : 0.039 0.157 845 Planarity : 0.004 0.054 956 Dihedral : 10.678 173.711 752 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.31 (0.25), residues: 415 sheet: -1.19 (0.69), residues: 57 loop : -1.30 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 6 HIS 0.010 0.002 HIS B 271 PHE 0.019 0.002 PHE B 13 TYR 0.018 0.002 TYR B 212 ARG 0.003 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.05571 ( 336) hydrogen bonds : angle 5.84038 ( 993) covalent geometry : bond 0.00252 ( 5584) covalent geometry : angle 0.56054 ( 7533) *********************** 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 110 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.911 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 125 LEU cc_start: 0.8503 (mt) cc_final: 0.8250 (mt) REVERT: B 223 MET cc_start: 0.9620 (mmp) cc_final: 0.9389 (mmm) REVERT: B 481 TYR cc_start: 0.6702 (m-10) cc_final: 0.6370 (m-10) REVERT: C 236 LEU cc_start: 0.6601 (tp) cc_final: 0.6110 (tp) REVERT: C 338 PHE cc_start: 0.7711 (m-10) cc_final: 0.7480 (m-80) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.4454 time to fit residues: 63.4063 Evaluate side-chains 94 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.057852 restraints weight = 107708.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060846 restraints weight = 64989.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063121 restraints weight = 43755.935| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5584 Z= 0.136 Angle : 0.533 6.032 7533 Z= 0.301 Chirality : 0.038 0.140 845 Planarity : 0.004 0.048 956 Dihedral : 10.042 158.998 752 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.32), residues: 664 helix: 0.61 (0.25), residues: 419 sheet: -1.09 (0.70), residues: 57 loop : -1.29 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 6 HIS 0.008 0.002 HIS B 419 PHE 0.019 0.002 PHE C 232 TYR 0.016 0.002 TYR B 169 ARG 0.003 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 336) hydrogen bonds : angle 5.59502 ( 993) covalent geometry : bond 0.00249 ( 5584) covalent geometry : angle 0.53303 ( 7533) *********************** 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 107 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.825 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: B 223 MET cc_start: 0.9627 (mmp) cc_final: 0.9420 (mmm) REVERT: B 481 TYR cc_start: 0.6747 (m-10) cc_final: 0.6402 (m-10) REVERT: C 107 CYS cc_start: 0.8018 (t) cc_final: 0.7646 (t) REVERT: C 232 PHE cc_start: 0.9274 (m-80) cc_final: 0.8552 (m-80) REVERT: C 236 LEU cc_start: 0.6887 (tp) cc_final: 0.6426 (tp) REVERT: C 338 PHE cc_start: 0.7590 (m-10) cc_final: 0.7359 (m-80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.4034 time to fit residues: 55.2951 Evaluate side-chains 95 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.077649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059227 restraints weight = 109851.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.061855 restraints weight = 70484.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.063838 restraints weight = 49242.288| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4441 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= 0.162 Angle : 0.545 5.701 7533 Z= 0.309 Chirality : 0.037 0.141 845 Planarity : 0.004 0.049 956 Dihedral : 9.584 166.786 752 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: -0.22 (0.32), residues: 664 helix: 0.66 (0.25), residues: 419 sheet: -1.39 (0.64), residues: 62 loop : -1.39 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 6 HIS 0.007 0.002 HIS B 419 PHE 0.011 0.002 PHE B 13 TYR 0.016 0.001 TYR B 169 ARG 0.003 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.04930 ( 336) hydrogen bonds : angle 5.57590 ( 993) covalent geometry : bond 0.00286 ( 5584) covalent geometry : angle 0.54497 ( 7533) *********************** 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 103 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 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: B 223 MET cc_start: 0.9589 (mmp) cc_final: 0.9345 (mmm) REVERT: B 481 TYR cc_start: 0.6502 (m-10) cc_final: 0.6157 (m-10) REVERT: C 232 PHE cc_start: 0.9070 (m-80) cc_final: 0.8378 (m-80) REVERT: C 236 LEU cc_start: 0.6971 (tp) cc_final: 0.6509 (tp) REVERT: C 338 PHE cc_start: 0.7645 (m-10) cc_final: 0.7367 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.5024 time to fit residues: 66.3636 Evaluate side-chains 87 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.077086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058301 restraints weight = 117441.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060845 restraints weight = 76516.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062822 restraints weight = 54268.423| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5584 Z= 0.180 Angle : 0.582 6.120 7533 Z= 0.326 Chirality : 0.038 0.181 845 Planarity : 0.004 0.051 956 Dihedral : 9.014 173.354 752 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % 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: -0.31 (0.32), residues: 664 helix: 0.61 (0.25), residues: 417 sheet: -1.19 (0.66), residues: 57 loop : -1.58 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 149 HIS 0.007 0.002 HIS B 419 PHE 0.011 0.002 PHE B 396 TYR 0.018 0.002 TYR B 169 ARG 0.003 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 336) hydrogen bonds : angle 5.63756 ( 993) covalent geometry : bond 0.00322 ( 5584) covalent geometry : angle 0.58180 ( 7533) *********************** 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 102 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 MET cc_start: 0.9585 (mmp) cc_final: 0.9341 (mmm) REVERT: B 315 ILE cc_start: 0.9485 (mm) cc_final: 0.9198 (mm) REVERT: B 318 CYS cc_start: 0.9398 (m) cc_final: 0.8990 (p) REVERT: C 232 PHE cc_start: 0.9093 (m-80) cc_final: 0.8451 (m-80) REVERT: C 236 LEU cc_start: 0.6985 (tp) cc_final: 0.6530 (tp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.5626 time to fit residues: 75.1409 Evaluate side-chains 85 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 229 HIS ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056542 restraints weight = 110862.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058982 restraints weight = 73111.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060861 restraints weight = 52158.511| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5584 Z= 0.199 Angle : 0.597 5.920 7533 Z= 0.339 Chirality : 0.039 0.182 845 Planarity : 0.004 0.053 956 Dihedral : 8.643 168.658 752 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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 : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.32), residues: 664 helix: 0.44 (0.25), residues: 419 sheet: -1.34 (0.66), residues: 57 loop : -1.70 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.007 0.002 HIS B 271 PHE 0.030 0.002 PHE B 430 TYR 0.017 0.002 TYR B 169 ARG 0.003 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 336) hydrogen bonds : angle 5.71472 ( 993) covalent geometry : bond 0.00351 ( 5584) covalent geometry : angle 0.59659 ( 7533) *********************** 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 102 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.241 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 223 MET cc_start: 0.9626 (mmp) cc_final: 0.9396 (mmm) REVERT: B 315 ILE cc_start: 0.9484 (mm) cc_final: 0.9224 (mm) REVERT: B 318 CYS cc_start: 0.9435 (m) cc_final: 0.8995 (p) REVERT: C 232 PHE cc_start: 0.9102 (m-80) cc_final: 0.8476 (m-80) REVERT: C 236 LEU cc_start: 0.6956 (tp) cc_final: 0.6353 (tp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.4958 time to fit residues: 65.3700 Evaluate side-chains 83 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.076660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057994 restraints weight = 114799.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.060640 restraints weight = 74592.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062616 restraints weight = 52798.309| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5584 Z= 0.170 Angle : 0.564 5.660 7533 Z= 0.319 Chirality : 0.038 0.139 845 Planarity : 0.004 0.053 956 Dihedral : 8.679 169.515 752 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % 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: -0.43 (0.32), residues: 664 helix: 0.53 (0.25), residues: 419 sheet: -1.36 (0.66), residues: 57 loop : -1.63 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.010 0.002 HIS B 479 PHE 0.020 0.002 PHE B 430 TYR 0.016 0.002 TYR B 317 ARG 0.006 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 336) hydrogen bonds : angle 5.62203 ( 993) covalent geometry : bond 0.00303 ( 5584) covalent geometry : angle 0.56438 ( 7533) *********************** 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 104 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.966 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 223 MET cc_start: 0.9618 (mmp) cc_final: 0.9393 (mmm) REVERT: C 232 PHE cc_start: 0.9130 (m-80) cc_final: 0.8519 (m-80) REVERT: C 236 LEU cc_start: 0.7009 (tp) cc_final: 0.6412 (tp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3912 time to fit residues: 52.5519 Evaluate side-chains 85 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.075983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057849 restraints weight = 112612.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060328 restraints weight = 73785.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062183 restraints weight = 52643.350| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5273 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= 0.150 Angle : 0.544 5.783 7533 Z= 0.305 Chirality : 0.038 0.134 845 Planarity : 0.004 0.052 956 Dihedral : 8.318 161.158 752 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.57 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: -0.25 (0.32), residues: 664 helix: 0.70 (0.26), residues: 419 sheet: -1.32 (0.67), residues: 57 loop : -1.62 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 149 HIS 0.006 0.001 HIS B 232 PHE 0.023 0.002 PHE B 430 TYR 0.017 0.002 TYR B 383 ARG 0.002 0.000 ARG B 443 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 336) hydrogen bonds : angle 5.50233 ( 993) covalent geometry : bond 0.00273 ( 5584) covalent geometry : angle 0.54365 ( 7533) ********************** 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 to be fit. rotamer outliers: 0 poor density : 106 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: B 223 MET cc_start: 0.9608 (mmp) cc_final: 0.9371 (mmm) REVERT: B 315 ILE cc_start: 0.9430 (mm) cc_final: 0.9148 (mm) REVERT: B 318 CYS cc_start: 0.9343 (m) cc_final: 0.8946 (p) REVERT: C 232 PHE cc_start: 0.9102 (m-80) cc_final: 0.8505 (m-80) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3946 time to fit residues: 53.9409 Evaluate side-chains 84 residues out of total 599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.076702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.058327 restraints weight = 106222.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060928 restraints weight = 69276.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.062861 restraints weight = 48828.304| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5584 Z= 0.129 Angle : 0.519 5.770 7533 Z= 0.288 Chirality : 0.037 0.135 845 Planarity : 0.004 0.051 956 Dihedral : 8.142 158.117 752 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: 0.12 (0.32), residues: 664 helix: 1.04 (0.26), residues: 411 sheet: -1.20 (0.68), residues: 56 loop : -1.49 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 6 HIS 0.006 0.001 HIS B 232 PHE 0.022 0.002 PHE B 430 TYR 0.014 0.001 TYR B 383 ARG 0.004 0.000 ARG B 443 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 336) hydrogen bonds : angle 5.35022 ( 993) covalent geometry : bond 0.00242 ( 5584) covalent geometry : angle 0.51881 ( 7533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4587.84 seconds wall clock time: 82 minutes 14.40 seconds (4934.40 seconds total)