Starting phenix.real_space_refine on Wed Jan 17 15:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/01_2024/6xqo_22291.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/01_2024/6xqo_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_22291/01_2024/6xqo_22291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/01_2024/6xqo_22291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/01_2024/6xqo_22291.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/01_2024/6xqo_22291.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. Process input model Symmetric amino acids flipped Residue "I ARG 154": "NH1" <-> "NH2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I GLU 298": "OE1" <-> "OE2" Residue "I ASP 306": "OD1" <-> "OD2" Residue "I ASP 316": "OD1" <-> "OD2" Residue "I TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 376": "OD1" <-> "OD2" Residue "I PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 423": "OD1" <-> "OD2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J GLU 380": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.68, per 1000 atoms: 0.62 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: 1.73 Conformation dependent library (CDL) restraints added in 722.4 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: 0.45 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: 1.18 Time building geometry restraints manager: 1.83 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 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 % Allowed : 18.78 % Favored : 77.70 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.003 0.001 HIS J 98 PHE 0.014 0.002 PHE I 367 TYR 0.010 0.001 TYR J 102 ARG 0.002 0.000 ARG I 401 *********************** 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 : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 348 GLN cc_start: 0.8191 (mm110) cc_final: 0.7934 (mm-40) REVERT: I 352 HIS cc_start: 0.7744 (m-70) cc_final: 0.7296 (m90) REVERT: I 438 LYS cc_start: 0.8440 (tttt) cc_final: 0.8125 (ttpt) REVERT: I 439 GLN cc_start: 0.8245 (pp30) cc_final: 0.7985 (pp30) REVERT: J 97 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5749 (pm20) REVERT: J 118 MET cc_start: 0.5977 (pp-130) cc_final: 0.5607 (pp-130) REVERT: J 202 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7480 (tptt) outliers start: 15 outliers final: 9 residues processed: 131 average time/residue: 0.2437 time to fit residues: 37.2476 Evaluate side-chains 109 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU 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: 0.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 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: 0.7405 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4382 Z= 0.297 Angle : 0.569 5.050 5914 Z= 0.310 Chirality : 0.040 0.122 669 Planarity : 0.004 0.037 762 Dihedral : 7.414 52.984 606 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.10 % Allowed : 19.25 % Favored : 74.65 % 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: -0.14 (0.26), residues: 372 sheet: None (None), residues: 0 loop : -1.69 (0.39), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 286 HIS 0.002 0.001 HIS J 384 PHE 0.016 0.002 PHE I 367 TYR 0.018 0.002 TYR J 249 ARG 0.006 0.001 ARG I 314 *********************** 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 136 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 438 LYS cc_start: 0.8519 (tttt) cc_final: 0.8272 (ttpt) REVERT: J 97 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5736 (pm20) REVERT: J 102 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: J 118 MET cc_start: 0.5862 (pp-130) cc_final: 0.5500 (pp-130) REVERT: J 170 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (mt) REVERT: J 202 LYS cc_start: 0.7846 (mmtt) cc_final: 0.7630 (tptt) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.2102 time to fit residues: 32.6755 Evaluate side-chains 123 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 17 optimal weight: 0.0670 chunk 40 optimal weight: 0.4980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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: 0.7348 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4382 Z= 0.181 Angle : 0.476 4.860 5914 Z= 0.262 Chirality : 0.036 0.118 669 Planarity : 0.004 0.040 762 Dihedral : 6.808 54.623 601 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.34 % Allowed : 20.19 % Favored : 73.47 % 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: -0.13 (0.34), residues: 546 helix: 0.55 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.38 (0.40), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 286 HIS 0.003 0.001 HIS J 178 PHE 0.015 0.001 PHE I 367 TYR 0.013 0.001 TYR I 130 ARG 0.005 0.001 ARG I 301 *********************** 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 133 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8694 (tptp) cc_final: 0.8343 (tptt) REVERT: I 346 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: I 386 MET cc_start: 0.8763 (ttm) cc_final: 0.8469 (ttm) REVERT: I 437 MET cc_start: 0.8873 (mmt) cc_final: 0.8595 (mmt) REVERT: I 438 LYS cc_start: 0.8504 (tttt) cc_final: 0.8250 (ttpt) REVERT: J 97 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5903 (pm20) REVERT: J 170 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7660 (mt) REVERT: J 201 GLN cc_start: 0.8423 (mm110) cc_final: 0.7558 (mt0) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.2267 time to fit residues: 32.4293 Evaluate side-chains 117 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 393 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 117 GLN J 235 GLN 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: 0.7414 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4382 Z= 0.312 Angle : 0.553 5.379 5914 Z= 0.306 Chirality : 0.040 0.125 669 Planarity : 0.004 0.045 762 Dihedral : 7.157 55.146 601 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.75 % Allowed : 20.66 % Favored : 71.60 % 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: 0.01 (0.35), residues: 546 helix: 0.61 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 300 HIS 0.003 0.001 HIS J 327 PHE 0.016 0.002 PHE I 367 TYR 0.012 0.002 TYR I 130 ARG 0.005 0.001 ARG I 301 *********************** 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 132 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8724 (tptp) cc_final: 0.8374 (tptt) REVERT: I 346 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: I 386 MET cc_start: 0.8710 (ttm) cc_final: 0.8386 (ttm) REVERT: I 438 LYS cc_start: 0.8555 (tttt) cc_final: 0.8307 (ttpt) REVERT: J 97 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: J 102 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: J 170 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7636 (mt) outliers start: 33 outliers final: 28 residues processed: 121 average time/residue: 0.2182 time to fit residues: 31.5829 Evaluate side-chains 128 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 393 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 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 264 GLN J 323 HIS ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2782 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= 0.256 Angle : 0.537 7.574 5914 Z= 0.294 Chirality : 0.038 0.124 669 Planarity : 0.004 0.049 762 Dihedral : 7.087 57.428 601 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.04 % Allowed : 21.13 % Favored : 71.83 % 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: 0.20 (0.35), residues: 546 helix: 0.76 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS J 174 PHE 0.016 0.002 PHE I 367 TYR 0.013 0.001 TYR I 130 ARG 0.004 0.001 ARG I 301 *********************** 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 125 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8745 (tptp) cc_final: 0.8371 (tptt) REVERT: I 346 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: I 386 MET cc_start: 0.8689 (ttm) cc_final: 0.8342 (ttm) REVERT: I 438 LYS cc_start: 0.8538 (tttt) cc_final: 0.8295 (ttpt) REVERT: J 97 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5850 (pm20) REVERT: J 170 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7584 (mt) REVERT: J 201 GLN cc_start: 0.8555 (mm110) cc_final: 0.7700 (mt0) outliers start: 30 outliers final: 25 residues processed: 116 average time/residue: 0.2121 time to fit residues: 29.3138 Evaluate side-chains 121 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 393 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 27 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS ** J 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2953 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= 0.215 Angle : 0.513 8.104 5914 Z= 0.278 Chirality : 0.037 0.119 669 Planarity : 0.004 0.047 762 Dihedral : 6.953 59.186 601 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 7.51 % Allowed : 21.60 % Favored : 70.89 % 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: 0.39 (0.35), residues: 546 helix: 0.88 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.06 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS J 174 PHE 0.015 0.001 PHE I 367 TYR 0.015 0.001 TYR I 130 ARG 0.004 0.001 ARG J 343 *********************** 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 131 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8761 (tptp) cc_final: 0.8394 (tptt) REVERT: I 346 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: I 381 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8018 (mp) REVERT: I 386 MET cc_start: 0.8688 (ttm) cc_final: 0.8309 (ttm) REVERT: I 438 LYS cc_start: 0.8550 (tttt) cc_final: 0.8308 (ttpt) REVERT: J 97 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5925 (pm20) REVERT: J 170 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7651 (mt) REVERT: J 201 GLN cc_start: 0.8533 (mm110) cc_final: 0.7653 (mt0) outliers start: 32 outliers final: 25 residues processed: 120 average time/residue: 0.2170 time to fit residues: 30.9115 Evaluate side-chains 124 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 393 ASN 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: 0.0670 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4382 Z= 0.204 Angle : 0.525 8.624 5914 Z= 0.281 Chirality : 0.037 0.117 669 Planarity : 0.004 0.048 762 Dihedral : 6.432 56.294 599 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.22 % Allowed : 21.83 % Favored : 69.95 % 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: 0.95 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.99 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS J 98 PHE 0.015 0.001 PHE I 367 TYR 0.016 0.001 TYR I 130 ARG 0.004 0.001 ARG I 325 *********************** 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 135 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8775 (tptp) cc_final: 0.8402 (tptt) REVERT: I 346 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: I 381 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7999 (mp) REVERT: I 386 MET cc_start: 0.8690 (ttm) cc_final: 0.8318 (ttm) REVERT: I 438 LYS cc_start: 0.8490 (tttt) cc_final: 0.8254 (ttpt) REVERT: J 97 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: J 170 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7660 (mt) REVERT: J 201 GLN cc_start: 0.8433 (mm110) cc_final: 0.7572 (mt0) REVERT: J 367 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8161 (mm) outliers start: 35 outliers final: 28 residues processed: 124 average time/residue: 0.2140 time to fit residues: 31.6120 Evaluate side-chains 128 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 393 ASN 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: 2.9990 chunk 33 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4382 Z= 0.226 Angle : 0.544 9.016 5914 Z= 0.292 Chirality : 0.037 0.138 669 Planarity : 0.004 0.050 762 Dihedral : 6.490 56.591 599 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 8.45 % Allowed : 21.60 % Favored : 69.95 % 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: 0.43 (0.35), residues: 546 helix: 0.90 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -1.00 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 174 PHE 0.015 0.001 PHE I 367 TYR 0.017 0.001 TYR I 130 ARG 0.005 0.001 ARG I 325 *********************** 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 133 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8763 (tptp) cc_final: 0.8370 (tptt) REVERT: I 346 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: I 381 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8000 (mp) REVERT: I 386 MET cc_start: 0.8693 (ttm) cc_final: 0.8301 (ttm) REVERT: I 438 LYS cc_start: 0.8522 (tttt) cc_final: 0.8294 (ttpt) REVERT: J 97 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: J 170 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7658 (mt) REVERT: J 367 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8167 (mm) outliers start: 36 outliers final: 27 residues processed: 121 average time/residue: 0.2104 time to fit residues: 30.2674 Evaluate side-chains 124 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 396 MET Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7380 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4382 Z= 0.243 Angle : 0.576 9.322 5914 Z= 0.307 Chirality : 0.038 0.136 669 Planarity : 0.004 0.049 762 Dihedral : 6.524 57.007 599 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 7.98 % Allowed : 21.83 % Favored : 70.19 % 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: 0.48 (0.35), residues: 546 helix: 0.91 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.94 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 174 PHE 0.015 0.001 PHE I 367 TYR 0.018 0.001 TYR I 130 ARG 0.017 0.001 ARG I 325 *********************** 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 128 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 341 LYS cc_start: 0.8777 (tptp) cc_final: 0.8365 (tptt) REVERT: I 346 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: I 381 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8001 (mp) REVERT: I 386 MET cc_start: 0.8685 (ttm) cc_final: 0.8307 (ttm) REVERT: I 438 LYS cc_start: 0.8534 (tttt) cc_final: 0.8305 (ttpt) REVERT: J 97 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6025 (pm20) REVERT: J 170 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7662 (mt) REVERT: J 367 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8171 (mm) outliers start: 34 outliers final: 27 residues processed: 118 average time/residue: 0.2153 time to fit residues: 30.1511 Evaluate side-chains 124 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 345 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 391 LEU 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: 0.9990 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7370 moved from start: 0.3257 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= 0.229 Angle : 0.575 9.477 5914 Z= 0.307 Chirality : 0.038 0.136 669 Planarity : 0.004 0.050 762 Dihedral : 6.455 57.301 599 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.51 % Allowed : 23.00 % Favored : 69.48 % 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: 0.51 (0.35), residues: 546 helix: 0.92 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.91 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS I 315 PHE 0.015 0.001 PHE I 367 TYR 0.010 0.001 TYR I 130 ARG 0.017 0.001 ARG I 325 ********************** 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 125 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 346 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: I 381 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7999 (mp) REVERT: I 386 MET cc_start: 0.8687 (ttm) cc_final: 0.8296 (ttm) REVERT: I 438 LYS cc_start: 0.8538 (tttt) cc_final: 0.8310 (ttpt) REVERT: J 97 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6040 (pm20) REVERT: J 170 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7657 (mt) REVERT: J 367 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8156 (mm) outliers start: 32 outliers final: 25 residues processed: 116 average time/residue: 0.2214 time to fit residues: 30.4839 Evaluate side-chains 121 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 296 PHE Chi-restraints excluded: chain I residue 308 LEU Chi-restraints excluded: chain I residue 311 GLU Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain I residue 381 LEU Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 192 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 272 SER Chi-restraints excluded: chain J residue 287 LEU Chi-restraints excluded: chain J residue 288 LEU Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 367 LEU Chi-restraints excluded: chain J residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.144984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124593 restraints weight = 7174.969| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.42 r_work: 0.3585 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3283 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= 0.233 Angle : 0.569 9.507 5914 Z= 0.304 Chirality : 0.038 0.134 669 Planarity : 0.004 0.050 762 Dihedral : 6.453 57.332 599 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 7.04 % Allowed : 23.24 % Favored : 69.72 % 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: 0.94 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 174 PHE 0.018 0.001 PHE J 289 TYR 0.009 0.001 TYR I 130 ARG 0.009 0.001 ARG I 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1400.38 seconds wall clock time: 25 minutes 49.90 seconds (1549.90 seconds total)