Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:08:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/11_2022/6x12_21986_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/11_2022/6x12_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_21986/11_2022/6x12_21986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/11_2022/6x12_21986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/11_2022/6x12_21986_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x12_21986/11_2022/6x12_21986_updated.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.32, per 1000 atoms: 0.76 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: 1.26 Conformation dependent library (CDL) restraints added in 464.6 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: 0.39 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: 0.80 Time building geometry restraints manager: 1.36 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: 1743 27.79 - 55.58: 80 55.58 - 83.38: 8 83.38 - 111.17: 1 111.17 - 138.96: 1 Dihedral angle restraints: 1833 sinusoidal: 678 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=" 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 dihedral pdb=" CA VAL A 235 " pdb=" C VAL A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 1830 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 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. 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: 0.740 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: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 15.873 138.961 1101 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 % 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 *********************** 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 : 0.349 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1566 time to fit residues: 11.3919 Evaluate side-chains 49 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4794 ------------------------------------------------------------------------------- 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: 0.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.0000 overall best weight: 0.4122 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.1602 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= 0.187 Angle : 0.545 6.285 4237 Z= 0.278 Chirality : 0.039 0.118 530 Planarity : 0.005 0.037 516 Dihedral : 9.528 80.340 459 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 3.15 % 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: -2.77 (0.38), residues: 403 helix: -1.55 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -2.21 (0.80), residues: 53 *********************** 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: 10 poor density : 53 time to evaluate : 0.360 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 61 average time/residue: 0.1729 time to fit residues: 12.6799 Evaluate side-chains 48 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0409 time to fit residues: 0.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.0010 chunk 12 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1988 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= 0.184 Angle : 0.538 6.109 4237 Z= 0.269 Chirality : 0.040 0.192 530 Planarity : 0.004 0.030 516 Dihedral : 8.213 52.438 459 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 3.15 % 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: -1.76 (0.41), residues: 403 helix: -0.79 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -2.39 (0.78), residues: 58 *********************** 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 58 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.340 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 57 average time/residue: 0.1455 time to fit residues: 10.3075 Evaluate side-chains 47 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.6461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.0020 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.3800 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3115 Z= 0.173 Angle : 0.525 5.987 4237 Z= 0.262 Chirality : 0.040 0.169 530 Planarity : 0.004 0.028 516 Dihedral : 7.718 55.103 459 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 2.21 % 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: -1.09 (0.42), residues: 403 helix: -0.37 (0.28), residues: 344 sheet: None (None), residues: 0 loop : -1.97 (0.81), residues: 59 *********************** 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 54 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.338 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 53 average time/residue: 0.1471 time to fit residues: 9.7264 Evaluate side-chains 46 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4129 time to fit residues: 0.8985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 3115 Z= 0.226 Angle : 0.548 6.096 4237 Z= 0.275 Chirality : 0.040 0.121 530 Planarity : 0.004 0.028 516 Dihedral : 7.633 55.159 459 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.42), residues: 403 helix: -0.18 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.84 (0.76), residues: 64 *********************** 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 53 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.361 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 51 average time/residue: 0.1814 time to fit residues: 11.4256 Evaluate side-chains 45 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0478 time to fit residues: 0.5283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3115 Z= 0.248 Angle : 0.563 6.090 4237 Z= 0.282 Chirality : 0.040 0.122 530 Planarity : 0.004 0.027 516 Dihedral : 7.492 54.750 459 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.21 % 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: -0.63 (0.43), residues: 403 helix: -0.03 (0.29), residues: 341 sheet: None (None), residues: 0 loop : -1.92 (0.78), residues: 62 *********************** 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 52 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.343 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.1487 time to fit residues: 9.4202 Evaluate side-chains 47 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0393 time to fit residues: 0.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.2529 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= 0.201 Angle : 0.550 6.600 4237 Z= 0.271 Chirality : 0.039 0.131 530 Planarity : 0.004 0.028 516 Dihedral : 7.199 55.522 459 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 1.58 % 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: -0.34 (0.43), residues: 403 helix: 0.15 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.65 (0.80), residues: 63 *********************** 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 50 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.349 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1426 time to fit residues: 8.6456 Evaluate side-chains 47 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0487 time to fit residues: 0.6169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 220 GLN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3115 Z= 0.155 Angle : 0.542 6.655 4237 Z= 0.268 Chirality : 0.039 0.163 530 Planarity : 0.004 0.028 516 Dihedral : 6.916 56.810 459 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.58 % 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: -0.10 (0.44), residues: 403 helix: 0.27 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -1.36 (0.86), residues: 60 *********************** 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 51 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.351 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.1528 time to fit residues: 9.2897 Evaluate side-chains 48 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0422 time to fit residues: 0.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.2730 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= 0.213 Angle : 0.598 11.389 4237 Z= 0.290 Chirality : 0.040 0.196 530 Planarity : 0.004 0.027 516 Dihedral : 7.097 55.920 459 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.43), residues: 403 helix: 0.30 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.69 (0.80), residues: 63 *********************** 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 47 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.337 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 0.1634 time to fit residues: 9.3150 Evaluate side-chains 45 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0536 time to fit residues: 0.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.0170 chunk 4 optimal weight: 0.0040 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.1438 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3115 Z= 0.133 Angle : 0.573 10.631 4237 Z= 0.278 Chirality : 0.039 0.196 530 Planarity : 0.004 0.028 516 Dihedral : 6.517 58.481 459 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.95 % 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: 0.42 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.20 (0.79), residues: 67 ********************** 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 55 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.342 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 0.1596 time to fit residues: 10.5179 Evaluate side-chains 46 residues out of total 317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 0.0070 chunk 1 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.2374 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.121029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.099254 restraints weight = 4468.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102108 restraints weight = 2418.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103925 restraints weight = 1682.542| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3115 Z= 0.151 Angle : 0.568 11.392 4237 Z= 0.275 Chirality : 0.039 0.189 530 Planarity : 0.004 0.027 516 Dihedral : 6.449 57.850 459 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.63 % 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: 0.23 (0.43), residues: 403 helix: 0.49 (0.29), residues: 337 sheet: None (None), residues: 0 loop : -1.08 (0.81), residues: 66 =============================================================================== Job complete usr+sys time: 1022.64 seconds wall clock time: 19 minutes 21.59 seconds (1161.59 seconds total)