Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:53:51 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/12_2021/6xqo_22291.pdb" } resolution = 3.1 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= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 4301 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2095 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 268} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "J" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2202 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 100 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.81, per 1000 atoms: 0.65 Number of scatterers: 4301 At special positions: 0 Unit cell: (60.648, 86.184, 100.016, 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) Ca 4 19.99 S 24 16.00 O 798 8.00 N 704 7.00 C 2771 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 Amimo 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: 1.97 Conformation dependent library (CDL) restraints added in 664.6 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 73.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'I' and resid 110 through 121 Processing helix chain 'I' and resid 123 through 132 Processing helix chain 'I' and resid 148 through 155 removed outlier: 3.555A pdb=" N PHE I 152 " --> pdb=" O THR I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 removed outlier: 3.690A pdb=" N THR I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 217 Processing helix chain 'I' and resid 219 through 231 removed outlier: 3.939A pdb=" N ILE I 225 " --> pdb=" O ARG I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 252 removed outlier: 3.753A pdb=" N PHE I 243 " --> pdb=" O ASP I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 292 through 314 removed outlier: 3.505A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU I 310 " --> pdb=" O ASP I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 339 through 353 removed outlier: 4.304A pdb=" N LYS I 350 " --> pdb=" O GLN I 346 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS I 351 " --> pdb=" O ARG I 347 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 373 removed outlier: 3.665A pdb=" N VAL I 364 " --> pdb=" O THR I 360 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN I 373 " --> pdb=" O THR I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 381 removed outlier: 3.756A pdb=" N THR I 379 " --> pdb=" O ASN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 387 Processing helix chain 'I' and resid 392 through 404 Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.611A pdb=" N CYS I 413 " --> pdb=" O SER I 409 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP I 421 " --> pdb=" O PHE I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.930A pdb=" N LEU I 441 " --> pdb=" O MET I 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 94 Processing helix chain 'J' and resid 105 through 115 removed outlier: 3.602A pdb=" N PHE J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 142 removed outlier: 4.160A pdb=" N ILE J 139 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA J 142 " --> pdb=" O GLY J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.140A pdb=" N THR J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 175 through 185 removed outlier: 4.702A pdb=" N VAL J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 211 removed outlier: 3.530A pdb=" N PHE J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS J 199 " --> pdb=" O ARG J 195 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU J 200 " --> pdb=" O GLU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 239 Processing helix chain 'J' and resid 248 through 272 Processing helix chain 'J' and resid 280 through 291 Processing helix chain 'J' and resid 296 through 306 removed outlier: 4.190A pdb=" N TRP J 300 " --> pdb=" O LYS J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 removed outlier: 3.599A pdb=" N PHE J 318 " --> pdb=" O SER J 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS J 327 " --> pdb=" O HIS J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 342 removed outlier: 5.258A pdb=" N MET J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 341 " --> pdb=" O MET J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 358 Processing helix chain 'J' and resid 363 through 374 removed outlier: 3.597A pdb=" N LEU J 367 " --> pdb=" O SER J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 392 removed outlier: 4.021A pdb=" N GLY J 389 " --> pdb=" O GLU J 385 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL J 390 " --> pdb=" O GLU J 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'J' and resid 278 through 279 249 hydrogen bonds defined for protein. 735 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: 1.14 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1388 1.34 - 1.46: 670 1.46 - 1.57: 2281 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 4382 Sorted by residual: bond pdb=" N THR J 232 " pdb=" CA THR J 232 " ideal model delta sigma weight residual 1.453 1.488 -0.036 1.31e-02 5.83e+03 7.39e+00 bond pdb=" N THR J 233 " pdb=" CA THR J 233 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" N ASN J 231 " pdb=" CA ASN J 231 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" CB GLU I 355 " pdb=" CG GLU I 355 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CA THR J 233 " pdb=" C THR J 233 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.24e-02 6.50e+03 9.29e-01 ... (remaining 4377 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.78: 60 106.78 - 113.56: 2371 113.56 - 120.35: 1773 120.35 - 127.13: 1689 127.13 - 133.92: 21 Bond angle restraints: 5914 Sorted by residual: angle pdb=" CA THR J 233 " pdb=" C THR J 233 " pdb=" O THR J 233 " ideal model delta sigma weight residual 121.00 116.89 4.11 1.05e+00 9.07e-01 1.53e+01 angle pdb=" CB GLU I 355 " pdb=" CG GLU I 355 " pdb=" CD GLU I 355 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 angle pdb=" CA THR J 232 " pdb=" C THR J 232 " pdb=" O THR J 232 " ideal model delta sigma weight residual 121.94 118.48 3.46 1.15e+00 7.56e-01 9.06e+00 angle pdb=" CA GLU I 355 " pdb=" CB GLU I 355 " pdb=" CG GLU I 355 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.75e+00 angle pdb=" C THR J 325 " pdb=" N THR J 326 " pdb=" CA THR J 326 " ideal model delta sigma weight residual 121.14 116.81 4.33 1.75e+00 3.27e-01 6.13e+00 ... (remaining 5909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2272 17.67 - 35.34: 216 35.34 - 53.01: 60 53.01 - 70.68: 9 70.68 - 88.35: 4 Dihedral angle restraints: 2561 sinusoidal: 938 harmonic: 1623 Sorted by residual: dihedral pdb=" CA MET J 104 " pdb=" C MET J 104 " pdb=" N THR J 105 " pdb=" CA THR J 105 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA MET J 278 " pdb=" C MET J 278 " pdb=" N ARG J 279 " pdb=" CA ARG J 279 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE J 277 " pdb=" C PHE J 277 " pdb=" N MET J 278 " pdb=" CA MET J 278 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 433 0.033 - 0.067: 171 0.067 - 0.100: 52 0.100 - 0.133: 11 0.133 - 0.167: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA GLU J 380 " pdb=" N GLU J 380 " pdb=" C GLU J 380 " pdb=" CB GLU J 380 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA THR J 232 " pdb=" N THR J 232 " pdb=" C THR J 232 " pdb=" CB THR J 232 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO J 106 " pdb=" N PRO J 106 " pdb=" C PRO J 106 " pdb=" CB PRO J 106 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 666 not shown) Planarity restraints: 762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG J 343 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO J 344 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO J 344 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 344 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 218 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 219 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 219 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 219 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 380 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" CD GLU J 380 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU J 380 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU J 380 " 0.008 2.00e-02 2.50e+03 ... (remaining 759 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 59 2.54 - 3.13: 3607 3.13 - 3.72: 6630 3.72 - 4.31: 8887 4.31 - 4.90: 14991 Nonbonded interactions: 34174 Sorted by model distance: nonbonded pdb=" OD1 ASN I 425 " pdb="CA CA I 502 " model vdw 1.956 2.510 nonbonded pdb=" OD1 ASN J 189 " pdb="CA CA J 501 " model vdw 2.146 2.510 nonbonded pdb=" OD1 ASP I 423 " pdb="CA CA I 502 " model vdw 2.193 2.510 nonbonded pdb=" O MET J 191 " pdb="CA CA J 501 " model vdw 2.194 2.510 nonbonded pdb=" O SER J 95 " pdb=" N LYS J 125 " model vdw 2.209 2.520 ... (remaining 34169 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 Ca 4 9.91 5 S 24 5.16 5 C 2771 2.51 5 N 704 2.21 5 O 798 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 individual isotropic Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.550 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.050 Process input model: 16.210 Find NCS groups from input model: 0.140 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:2.160 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 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 : 0.004 0.037 4382 Z= 0.273 Angle : 0.573 5.584 5914 Z= 0.337 Chirality : 0.040 0.167 669 Planarity : 0.003 0.038 762 Dihedral : 15.615 88.352 1503 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -2.83 (0.29), residues: 546 helix: -1.52 (0.23), residues: 369 sheet: None (None), residues: 0 loop : -2.34 (0.36), residues: 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.2374 time to fit residues: 36.2988 Evaluate side-chains 102 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1003 time to fit residues: 1.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 222 ASN ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 GLN I 411 HIS I 430 ASN J 235 GLN J 264 GLN J 292 ASN J 323 HIS J 327 HIS J 384 HIS J 393 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 4382 Z= 0.244 Angle : 0.548 4.908 5914 Z= 0.298 Chirality : 0.039 0.120 669 Planarity : 0.004 0.042 762 Dihedral : 4.334 17.380 584 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.96 (0.33), residues: 546 helix: -0.11 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.62 (0.38), residues: 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 0.2107 time to fit residues: 30.9524 Evaluate side-chains 110 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0519 time to fit residues: 1.6721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 54 optimal weight: 0.0870 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 300 GLN J 178 HIS J 235 GLN ** J 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 384 HIS ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 4382 Z= 0.166 Angle : 0.469 4.712 5914 Z= 0.258 Chirality : 0.035 0.110 669 Planarity : 0.004 0.060 762 Dihedral : 3.876 15.694 584 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.05 (0.34), residues: 546 helix: 0.62 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.14 (0.40), residues: 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.2376 time to fit residues: 30.0904 Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0490 time to fit residues: 1.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 47 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 117 GLN J 264 GLN ** J 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 323 HIS ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 4382 Z= 0.210 Angle : 0.489 5.010 5914 Z= 0.269 Chirality : 0.037 0.115 669 Planarity : 0.004 0.061 762 Dihedral : 3.979 17.465 584 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 (0.35), residues: 546 helix: 0.81 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.2296 time to fit residues: 28.8235 Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0541 time to fit residues: 1.0950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.0010 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4382 Z= 0.184 Angle : 0.503 7.800 5914 Z= 0.275 Chirality : 0.036 0.109 669 Planarity : 0.004 0.061 762 Dihedral : 3.854 17.387 584 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.56 (0.35), residues: 546 helix: 0.95 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.80 (0.42), residues: 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.2256 time to fit residues: 26.8927 Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0430 time to fit residues: 0.8688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4382 Z= 0.181 Angle : 0.492 7.505 5914 Z= 0.267 Chirality : 0.035 0.113 669 Planarity : 0.004 0.064 762 Dihedral : 3.730 17.569 584 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.68 (0.35), residues: 546 helix: 1.06 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 103 average time/residue: 0.2187 time to fit residues: 26.8693 Evaluate side-chains 97 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0720 time to fit residues: 1.0022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4382 Z= 0.262 Angle : 0.564 8.537 5914 Z= 0.301 Chirality : 0.038 0.113 669 Planarity : 0.004 0.065 762 Dihedral : 3.999 18.232 584 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.57 (0.35), residues: 546 helix: 0.97 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.80 (0.42), residues: 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.526 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.2258 time to fit residues: 26.0951 Evaluate side-chains 94 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0568 time to fit residues: 0.9436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4382 Z= 0.208 Angle : 0.547 9.132 5914 Z= 0.290 Chirality : 0.036 0.118 669 Planarity : 0.004 0.062 762 Dihedral : 3.820 17.897 584 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.74 (0.35), residues: 546 helix: 1.08 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.2311 time to fit residues: 26.6370 Evaluate side-chains 93 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0607 time to fit residues: 0.8426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4382 Z= 0.235 Angle : 0.573 9.058 5914 Z= 0.304 Chirality : 0.037 0.143 669 Planarity : 0.004 0.067 762 Dihedral : 3.900 18.097 584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 (0.35), residues: 546 helix: 1.00 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.82 (0.43), residues: 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.2348 time to fit residues: 26.4403 Evaluate side-chains 92 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0580 time to fit residues: 0.8154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 46 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4382 Z= 0.193 Angle : 0.555 9.363 5914 Z= 0.293 Chirality : 0.036 0.137 669 Planarity : 0.004 0.067 762 Dihedral : 3.726 17.589 584 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.79 (0.35), residues: 546 helix: 1.11 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.72 (0.44), residues: 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.2277 time to fit residues: 25.5076 Evaluate side-chains 90 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0576 time to fit residues: 0.9004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 38 optimal weight: 0.0000 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.147188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126358 restraints weight = 7363.988| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.48 r_work: 0.3707 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3683 rms_B_bonded: 2.31 restraints_weight: 0.1250 r_work: 0.3671 rms_B_bonded: 2.43 restraints_weight: 0.0625 r_work: 0.3656 rms_B_bonded: 2.60 restraints_weight: 0.0312 r_work: 0.3641 rms_B_bonded: 2.82 restraints_weight: 0.0156 r_work: 0.3624 rms_B_bonded: 3.10 restraints_weight: 0.0078 r_work: 0.3606 rms_B_bonded: 3.43 restraints_weight: 0.0039 r_work: 0.3585 rms_B_bonded: 3.83 restraints_weight: 0.0020 r_work: 0.3562 rms_B_bonded: 4.31 restraints_weight: 0.0010 r_work: 0.3537 rms_B_bonded: 4.87 restraints_weight: 0.0005 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4382 Z= 0.227 Angle : 0.571 9.313 5914 Z= 0.303 Chirality : 0.037 0.136 669 Planarity : 0.004 0.069 762 Dihedral : 3.844 18.050 584 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.73 (0.35), residues: 546 helix: 1.07 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.75 (0.43), residues: 167 =============================================================================== Job complete usr+sys time: 1302.99 seconds wall clock time: 24 minutes 24.79 seconds (1464.79 seconds total)