Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:28:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/11_2022/6xqo_22291.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/11_2022/6xqo_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_22291/11_2022/6xqo_22291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/11_2022/6xqo_22291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/11_2022/6xqo_22291.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/11_2022/6xqo_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 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 "J PHE 268": "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: 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: {'CIS': 1, 'PTRANS': 4, '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: 3.05, per 1000 atoms: 0.71 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 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: 1.83 Conformation dependent library (CDL) restraints added in 616.6 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: 0.23 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: 1.20 Time building geometry restraints manager: 1.96 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 Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.570 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.040 Process input model: 16.660 Find NCS groups from input model: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.2388 time to fit residues: 36.5564 Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1019 time to fit residues: 1.9881 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7561 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 4382 Z= 0.299 Angle : 0.583 5.545 5914 Z= 0.316 Chirality : 0.040 0.126 669 Planarity : 0.004 0.038 762 Dihedral : 4.497 17.610 584 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 5.16 % 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: -1.02 (0.33), residues: 546 helix: -0.17 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -1.59 (0.39), residues: 175 *********************** 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 130 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 0.2098 time to fit residues: 30.8319 Evaluate side-chains 113 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0490 time to fit residues: 1.8021 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 HIS J 235 GLN J 323 HIS J 384 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 4382 Z= 0.265 Angle : 0.534 5.137 5914 Z= 0.294 Chirality : 0.038 0.126 669 Planarity : 0.004 0.041 762 Dihedral : 4.302 17.299 584 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 2.82 % 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: -0.32 (0.34), residues: 546 helix: 0.37 (0.27), residues: 372 sheet: None (None), residues: 0 loop : -1.37 (0.40), residues: 174 *********************** 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 114 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 107 average time/residue: 0.2146 time to fit residues: 27.4528 Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0467 time to fit residues: 1.2227 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 0.0050 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 300 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4382 Z= 0.231 Angle : 0.525 6.846 5914 Z= 0.288 Chirality : 0.037 0.119 669 Planarity : 0.004 0.043 762 Dihedral : 4.146 17.343 584 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -0.03 (0.35), residues: 546 helix: 0.54 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 172 *********************** 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 110 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.2142 time to fit residues: 27.7368 Evaluate side-chains 99 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0514 time to fit residues: 1.1457 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7558 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4382 Z= 0.282 Angle : 0.555 5.948 5914 Z= 0.305 Chirality : 0.039 0.123 669 Planarity : 0.004 0.043 762 Dihedral : 4.235 17.788 584 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.08 (0.35), residues: 546 helix: 0.63 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.08 (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 99 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.2163 time to fit residues: 25.2076 Evaluate side-chains 95 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.481 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0437 time to fit residues: 1.0017 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 4382 Z= 0.227 Angle : 0.533 7.515 5914 Z= 0.289 Chirality : 0.038 0.117 669 Planarity : 0.004 0.047 762 Dihedral : 4.059 17.464 584 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.38 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: 0.25 (0.35), residues: 546 helix: 0.74 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.00 (0.43), 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 104 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.2148 time to fit residues: 26.7443 Evaluate side-chains 96 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0519 time to fit residues: 0.9790 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7517 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4382 Z= 0.205 Angle : 0.534 8.483 5914 Z= 0.287 Chirality : 0.037 0.114 669 Planarity : 0.004 0.048 762 Dihedral : 3.904 17.384 584 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.88 % 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: 0.47 (0.35), residues: 546 helix: 0.90 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 171 *********************** 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 106 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.2172 time to fit residues: 26.0253 Evaluate side-chains 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0424 time to fit residues: 0.8309 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 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: 0.7547 moved from start: 0.3168 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= 0.267 Angle : 0.575 9.117 5914 Z= 0.309 Chirality : 0.038 0.128 669 Planarity : 0.004 0.047 762 Dihedral : 4.034 15.115 584 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.17 % 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: 0.35 (0.35), residues: 546 helix: 0.82 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 170 *********************** 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 96 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.539 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 96 average time/residue: 0.2222 time to fit residues: 25.4750 Evaluate side-chains 91 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0488 time to fit residues: 0.8791 ------------------------------------------------------------------------------- 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: 0.4980 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 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: 0.7518 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4382 Z= 0.212 Angle : 0.576 9.109 5914 Z= 0.302 Chirality : 0.037 0.120 669 Planarity : 0.004 0.048 762 Dihedral : 3.925 16.196 584 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.17 % 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: 0.49 (0.35), residues: 546 helix: 0.89 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.85 (0.44), 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 98 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.523 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 96 average time/residue: 0.2301 time to fit residues: 26.3270 Evaluate side-chains 88 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0491 time to fit residues: 0.8192 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.7529 moved from start: 0.3418 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= 0.238 Angle : 0.590 9.443 5914 Z= 0.311 Chirality : 0.037 0.116 669 Planarity : 0.004 0.047 762 Dihedral : 3.980 16.786 584 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.41 (0.35), residues: 546 helix: 0.85 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.95 (0.44), residues: 166 ********************** 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 88 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 88 average time/residue: 0.2368 time to fit residues: 24.6801 Evaluate side-chains 85 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0790 time to fit residues: 0.8539 ------------------------------------------------------------------------------- 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: 0.7980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.0470 chunk 38 optimal weight: 0.0470 chunk 2 optimal weight: 0.0270 chunk 31 optimal weight: 3.9990 overall best weight: 0.3234 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.147586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.127144 restraints weight = 7155.027| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.42 r_work: 0.3721 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work: 0.3698 rms_B_bonded: 2.25 restraints_weight: 0.1250 r_work: 0.3685 rms_B_bonded: 2.37 restraints_weight: 0.0625 r_work: 0.3671 rms_B_bonded: 2.54 restraints_weight: 0.0312 r_work: 0.3656 rms_B_bonded: 2.76 restraints_weight: 0.0156 r_work: 0.3640 rms_B_bonded: 3.03 restraints_weight: 0.0078 r_work: 0.3621 rms_B_bonded: 3.36 restraints_weight: 0.0039 r_work: 0.3601 rms_B_bonded: 3.75 restraints_weight: 0.0020 r_work: 0.3579 rms_B_bonded: 4.21 restraints_weight: 0.0010 r_work: 0.3554 rms_B_bonded: 4.75 restraints_weight: 0.0005 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3623 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= 0.199 Angle : 0.591 9.362 5914 Z= 0.307 Chirality : 0.036 0.125 669 Planarity : 0.004 0.062 762 Dihedral : 3.830 16.475 584 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.00 % 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: 0.53 (0.35), residues: 546 helix: 0.92 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -0.79 (0.44), residues: 172 =============================================================================== Job complete usr+sys time: 1268.54 seconds wall clock time: 23 minutes 48.17 seconds (1428.17 seconds total)