Starting phenix.real_space_refine on Sun Mar 10 15:36:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/03_2024/6x12_21986_updated.pdb" } resolution = 3.52 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 2019 2.51 5 N 486 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3059 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3059 Unusual residues: {'6OU': 1} Classifications: {'peptide': 407, 'undetermined': 1} Link IDs: {'PTRANS': 17, 'TRANS': 389, None: 1} Not linked: pdbres="GLY A 417 " pdbres="6OU A 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.26, per 1000 atoms: 0.74 Number of scatterers: 3059 At special positions: 0 Unit cell: (67.6148, 79.4205, 69.7613, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 535 8.00 N 486 7.00 C 2019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 636.0 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.791A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.518A pdb=" N THR A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.897A pdb=" N ASP A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU A 49 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.531A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 106 removed outlier: 3.557A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.635A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.526A pdb=" N ILE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 219 removed outlier: 3.631A pdb=" N VAL A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.827A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 5.666A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Proline residue: A 283 - end of helix removed outlier: 3.805A pdb=" N MET A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Proline residue: A 304 - end of helix removed outlier: 3.725A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 removed outlier: 4.277A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.078A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.228A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 416 removed outlier: 3.890A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 522 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: 0.78 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 469 1.31 - 1.43: 763 1.43 - 1.56: 1835 1.56 - 1.68: 14 1.68 - 1.81: 34 Bond restraints: 3115 Sorted by residual: bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.409 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C39 6OU A 501 " pdb=" C40 6OU A 501 " ideal model delta sigma weight residual 1.497 1.569 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C15 6OU A 501 " pdb=" C16 6OU A 501 " ideal model delta sigma weight residual 1.501 1.563 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C38 6OU A 501 " pdb=" C39 6OU A 501 " ideal model delta sigma weight residual 1.530 1.582 -0.052 2.00e-02 2.50e+03 6.85e+00 ... (remaining 3110 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.47: 76 105.47 - 112.15: 1568 112.15 - 118.82: 952 118.82 - 125.50: 1610 125.50 - 132.17: 31 Bond angle restraints: 4237 Sorted by residual: angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 108.77 -14.82 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N THR A 375 " pdb=" CA THR A 375 " pdb=" C THR A 375 " ideal model delta sigma weight residual 114.04 108.42 5.62 1.24e+00 6.50e-01 2.05e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 119.02 -9.21 2.21e+00 2.05e-01 1.74e+01 angle pdb=" C THR A 308 " pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 122.95 118.55 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" C THR A 281 " pdb=" N LEU A 282 " pdb=" CA LEU A 282 " ideal model delta sigma weight residual 120.09 124.47 -4.38 1.25e+00 6.40e-01 1.23e+01 ... (remaining 4232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.79: 1748 27.79 - 55.58: 82 55.58 - 83.38: 10 83.38 - 111.17: 3 111.17 - 138.96: 1 Dihedral angle restraints: 1844 sinusoidal: 689 harmonic: 1155 Sorted by residual: dihedral pdb=" C43 6OU A 501 " pdb=" C44 6OU A 501 " pdb=" C45 6OU A 501 " pdb=" C46 6OU A 501 " ideal model delta sinusoidal sigma weight residual -178.62 -39.66 -138.96 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C19 6OU A 501 " pdb=" C20 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O22 6OU A 501 " ideal model delta sinusoidal sigma weight residual -59.00 35.22 -94.22 1 3.00e+01 1.11e-03 1.15e+01 dihedral pdb=" CA THR A 154 " pdb=" C THR A 154 " pdb=" N ILE A 155 " pdb=" CA ILE A 155 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 1841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 413 0.061 - 0.121: 96 0.121 - 0.182: 17 0.182 - 0.242: 2 0.242 - 0.302: 2 Chirality restraints: 530 Sorted by residual: chirality pdb=" CB ILE A 113 " pdb=" CA ILE A 113 " pdb=" CG1 ILE A 113 " pdb=" CG2 ILE A 113 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 309 " pdb=" CA ILE A 309 " pdb=" CG1 ILE A 309 " pdb=" CG2 ILE A 309 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C20 6OU A 501 " pdb=" C19 6OU A 501 " pdb=" C21 6OU A 501 " pdb=" O30 6OU A 501 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 527 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 356 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 153 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 206 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.034 5.00e-02 4.00e+02 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 967 2.84 - 3.35: 2906 3.35 - 3.87: 4976 3.87 - 4.38: 5577 4.38 - 4.90: 9603 Nonbonded interactions: 24029 Sorted by model distance: nonbonded pdb=" O SER A 349 " pdb=" OG SER A 349 " model vdw 2.322 2.440 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.387 2.440 nonbonded pdb=" NZ LYS A 84 " pdb=" OE2 GLU A 416 " model vdw 2.398 2.520 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.423 2.440 nonbonded pdb=" OD2 ASP A 267 " pdb=" NH2 ARG A 287 " model vdw 2.424 2.520 ... (remaining 24024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.000 Extract box with map and model: 3.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.008 0.088 3115 Z= 0.525 Angle : 1.079 14.824 4237 Z= 0.580 Chirality : 0.056 0.302 530 Planarity : 0.008 0.063 516 Dihedral : 16.636 138.961 1112 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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: -5.29 (0.27), residues: 403 helix: -3.21 (0.17), residues: 348 sheet: None (None), residues: 0 loop : -3.27 (0.66), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 223 PHE 0.010 0.002 PHE A 210 TYR 0.026 0.002 TYR A 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.300 Fit side-chains REVERT: A 5 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7616 (mtt-85) REVERT: A 37 HIS cc_start: 0.7841 (t70) cc_final: 0.7585 (p90) REVERT: A 136 ASP cc_start: 0.8232 (m-30) cc_final: 0.7670 (m-30) REVERT: A 316 LEU cc_start: 0.9196 (mt) cc_final: 0.8985 (mm) REVERT: A 347 LEU cc_start: 0.9059 (tp) cc_final: 0.8818 (tt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1789 time to fit residues: 12.8802 Evaluate side-chains 51 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 0.0370 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3115 Z= 0.177 Angle : 0.539 6.242 4237 Z= 0.276 Chirality : 0.039 0.118 530 Planarity : 0.005 0.036 516 Dihedral : 10.574 85.543 470 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.84 % Allowed : 12.62 % Favored : 84.54 % 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: -2.81 (0.38), residues: 403 helix: -1.56 (0.25), residues: 353 sheet: None (None), residues: 0 loop : -2.38 (0.83), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.005 0.001 PHE A 324 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.315 Fit side-chains REVERT: A 5 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7629 (mtt-85) REVERT: A 37 HIS cc_start: 0.7814 (t70) cc_final: 0.7514 (p-80) REVERT: A 136 ASP cc_start: 0.8300 (m-30) cc_final: 0.7741 (m-30) REVERT: A 269 MET cc_start: 0.8179 (ttm) cc_final: 0.7741 (ttp) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.1825 time to fit residues: 13.5910 Evaluate side-chains 47 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3115 Z= 0.204 Angle : 0.549 6.089 4237 Z= 0.273 Chirality : 0.040 0.205 530 Planarity : 0.004 0.030 516 Dihedral : 9.375 89.713 470 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.42 % Allowed : 13.88 % Favored : 81.70 % 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: -1.78 (0.41), residues: 403 helix: -0.80 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -2.57 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 368 PHE 0.011 0.001 PHE A 324 TYR 0.018 0.001 TYR A 299 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.335 Fit side-chains REVERT: A 5 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7513 (mtt-85) REVERT: A 54 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7919 (mt) REVERT: A 136 ASP cc_start: 0.8367 (m-30) cc_final: 0.7839 (m-30) REVERT: A 269 MET cc_start: 0.8264 (ttm) cc_final: 0.7781 (ttp) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.1400 time to fit residues: 10.4261 Evaluate side-chains 54 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3115 Z= 0.244 Angle : 0.557 6.061 4237 Z= 0.276 Chirality : 0.041 0.184 530 Planarity : 0.004 0.028 516 Dihedral : 9.095 88.894 470 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.42 % Allowed : 15.46 % Favored : 80.13 % 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: -1.31 (0.42), residues: 403 helix: -0.45 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -2.57 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 368 PHE 0.010 0.001 PHE A 324 TYR 0.020 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.313 Fit side-chains REVERT: A 5 ARG cc_start: 0.7764 (mtt90) cc_final: 0.7535 (mtt-85) REVERT: A 54 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 220 GLN cc_start: 0.8291 (mm-40) cc_final: 0.7512 (mt0) REVERT: A 269 MET cc_start: 0.8358 (ttm) cc_final: 0.7849 (ttp) outliers start: 14 outliers final: 7 residues processed: 58 average time/residue: 0.1343 time to fit residues: 9.6434 Evaluate side-chains 53 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3115 Z= 0.206 Angle : 0.534 6.126 4237 Z= 0.266 Chirality : 0.039 0.112 530 Planarity : 0.004 0.027 516 Dihedral : 8.676 86.019 470 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.10 % Allowed : 16.72 % Favored : 79.18 % 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: -0.93 (0.42), residues: 403 helix: -0.21 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -2.32 (0.80), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 368 PHE 0.007 0.001 PHE A 324 TYR 0.019 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.340 Fit side-chains REVERT: A 5 ARG cc_start: 0.7751 (mtt90) cc_final: 0.7530 (mtt-85) REVERT: A 54 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (mt) REVERT: A 220 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7592 (mt0) REVERT: A 269 MET cc_start: 0.8377 (ttm) cc_final: 0.7856 (ttp) REVERT: A 275 THR cc_start: 0.9018 (t) cc_final: 0.8811 (t) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.1430 time to fit residues: 10.4644 Evaluate side-chains 53 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3115 Z= 0.218 Angle : 0.541 6.146 4237 Z= 0.268 Chirality : 0.040 0.104 530 Planarity : 0.004 0.028 516 Dihedral : 8.441 84.406 470 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.79 % Allowed : 18.30 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.42), residues: 403 helix: -0.08 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -2.12 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 368 PHE 0.006 0.001 PHE A 324 TYR 0.020 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.394 Fit side-chains REVERT: A 5 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7529 (mtt-85) REVERT: A 220 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7622 (mt0) REVERT: A 241 LEU cc_start: 0.8958 (tp) cc_final: 0.8681 (tp) REVERT: A 269 MET cc_start: 0.8393 (ttm) cc_final: 0.7892 (ttp) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.1465 time to fit residues: 10.3991 Evaluate side-chains 51 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3115 Z= 0.163 Angle : 0.518 6.105 4237 Z= 0.255 Chirality : 0.039 0.117 530 Planarity : 0.003 0.027 516 Dihedral : 8.076 80.303 470 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.47 % Allowed : 18.61 % Favored : 77.92 % 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 (0.43), residues: 403 helix: 0.14 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.57 (0.85), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 223 PHE 0.005 0.001 PHE A 273 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.333 Fit side-chains REVERT: A 5 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7500 (mtt-85) REVERT: A 80 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8410 (tmm-80) REVERT: A 220 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7630 (mt0) REVERT: A 241 LEU cc_start: 0.8955 (tp) cc_final: 0.8667 (tp) REVERT: A 269 MET cc_start: 0.8377 (ttm) cc_final: 0.7877 (ttp) REVERT: A 275 THR cc_start: 0.8947 (t) cc_final: 0.8729 (t) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1395 time to fit residues: 9.7427 Evaluate side-chains 51 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3115 Z= 0.184 Angle : 0.542 6.662 4237 Z= 0.264 Chirality : 0.039 0.103 530 Planarity : 0.003 0.027 516 Dihedral : 8.023 80.181 470 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 19.87 % Favored : 77.60 % 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: -0.15 (0.43), residues: 403 helix: 0.24 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.47 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 223 PHE 0.005 0.001 PHE A 273 TYR 0.019 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.335 Fit side-chains REVERT: A 5 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7512 (mtt-85) REVERT: A 80 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8393 (tmm-80) REVERT: A 220 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7659 (mt0) REVERT: A 241 LEU cc_start: 0.8957 (tp) cc_final: 0.8663 (tp) REVERT: A 269 MET cc_start: 0.8399 (ttm) cc_final: 0.7885 (ttp) REVERT: A 275 THR cc_start: 0.8941 (t) cc_final: 0.8709 (t) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 0.1481 time to fit residues: 9.7081 Evaluate side-chains 51 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3115 Z= 0.213 Angle : 0.559 7.454 4237 Z= 0.274 Chirality : 0.039 0.104 530 Planarity : 0.004 0.027 516 Dihedral : 8.128 80.947 470 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.15 % Allowed : 19.56 % Favored : 77.29 % 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 (0.43), residues: 403 helix: 0.26 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.41 (0.89), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 223 PHE 0.006 0.001 PHE A 273 TYR 0.021 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.342 Fit side-chains REVERT: A 5 ARG cc_start: 0.7733 (mtt90) cc_final: 0.7517 (mtt-85) REVERT: A 80 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8393 (tmm-80) REVERT: A 220 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7635 (mt0) REVERT: A 241 LEU cc_start: 0.8968 (tp) cc_final: 0.8658 (tp) REVERT: A 269 MET cc_start: 0.8402 (ttm) cc_final: 0.7980 (ttp) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1496 time to fit residues: 9.6299 Evaluate side-chains 50 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.0770 chunk 1 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3115 Z= 0.165 Angle : 0.538 7.916 4237 Z= 0.263 Chirality : 0.039 0.118 530 Planarity : 0.003 0.027 516 Dihedral : 7.852 76.209 470 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.52 % Allowed : 19.56 % Favored : 77.92 % 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: 0.08 (0.44), residues: 403 helix: 0.38 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.27 (0.89), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 223 PHE 0.007 0.001 PHE A 273 TYR 0.020 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.338 Fit side-chains REVERT: A 5 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7503 (mtt-85) REVERT: A 80 ARG cc_start: 0.8722 (tmm-80) cc_final: 0.8347 (tmm-80) REVERT: A 220 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7663 (mt0) REVERT: A 241 LEU cc_start: 0.8905 (tp) cc_final: 0.8598 (tp) REVERT: A 269 MET cc_start: 0.8381 (ttm) cc_final: 0.7957 (ttp) REVERT: A 275 THR cc_start: 0.8909 (t) cc_final: 0.8675 (t) outliers start: 8 outliers final: 5 residues processed: 51 average time/residue: 0.1558 time to fit residues: 9.8776 Evaluate side-chains 49 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 215 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097324 restraints weight = 4530.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100179 restraints weight = 2421.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101963 restraints weight = 1681.278| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3115 Z= 0.141 Angle : 0.545 12.098 4237 Z= 0.262 Chirality : 0.038 0.102 530 Planarity : 0.003 0.028 516 Dihedral : 7.592 71.124 470 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 19.87 % Favored : 77.29 % 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: 0.21 (0.44), residues: 403 helix: 0.46 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -1.19 (0.90), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 223 PHE 0.006 0.001 PHE A 273 TYR 0.019 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1077.43 seconds wall clock time: 20 minutes 0.66 seconds (1200.66 seconds total)