Starting phenix.real_space_refine on Mon Sep 23 18:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/09_2024/6xqo_22291.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/09_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_22291/09_2024/6xqo_22291.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/09_2024/6xqo_22291.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/09_2024/6xqo_22291.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xqo_22291/09_2024/6xqo_22291.cif" } 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. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.09, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 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: 1.05 Conformation dependent library (CDL) restraints added in 548.3 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: 0.41 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: 0.92 Time building geometry restraints manager: 1.24 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: 0.00 - 1.12: 5604 1.12 - 2.23: 247 2.23 - 3.35: 44 3.35 - 4.47: 13 4.47 - 5.58: 6 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 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.870 Find NCS groups from input model: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- 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 : 0.457 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: 0.2424 time to fit residues: 37.0421 Evaluate side-chains 109 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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: 0.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 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: I 222 ASN ** I 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 HIS I 430 ASN J 235 GLN J 264 GLN J 323 HIS J 327 HIS J 384 HIS J 393 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4382 Z= 0.260 Angle : 0.560 5.310 5914 Z= 0.307 Chirality : 0.040 0.121 669 Planarity : 0.004 0.041 762 Dihedral : 7.287 52.316 606 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.26 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: -0.94 (0.33), residues: 546 helix: -0.11 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.58 (0.39), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 286 HIS 0.003 0.001 HIS J 174 PHE 0.015 0.002 PHE I 367 TYR 0.019 0.002 TYR J 249 ARG 0.007 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 139 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 437 MET cc_start: 0.8895 (mmt) cc_final: 0.8555 (mmt) REVERT: I 438 LYS cc_start: 0.8514 (tttt) cc_final: 0.8254 (ttpt) REVERT: J 97 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: J 102 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: J 118 MET cc_start: 0.5836 (pp-130) cc_final: 0.5540 (pp-130) REVERT: J 170 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7645 (mt) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.2098 time to fit residues: 33.2230 Evaluate side-chains 120 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 J 384 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2650 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= 0.178 Angle : 0.483 5.505 5914 Z= 0.266 Chirality : 0.036 0.117 669 Planarity : 0.004 0.049 762 Dihedral : 6.845 54.423 601 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.40 % Allowed : 19.72 % Favored : 74.88 % 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: -0.09 (0.34), residues: 546 helix: 0.53 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 286 HIS 0.002 0.001 HIS J 178 PHE 0.014 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 132 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 381 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8001 (mp) REVERT: I 386 MET cc_start: 0.8731 (ttm) cc_final: 0.8464 (ttm) REVERT: I 438 LYS cc_start: 0.8552 (tttt) cc_final: 0.8242 (ttpt) REVERT: J 86 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7107 (mmt-90) REVERT: J 97 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6034 (pm20) REVERT: J 170 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7685 (mt) REVERT: J 201 GLN cc_start: 0.8442 (mm110) cc_final: 0.7435 (mt0) REVERT: J 265 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6790 (mt-10) outliers start: 23 outliers final: 17 residues processed: 125 average time/residue: 0.2183 time to fit residues: 32.4706 Evaluate side-chains 118 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 360 THR 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 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 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: 0.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2776 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= 0.268 Angle : 0.537 5.757 5914 Z= 0.296 Chirality : 0.039 0.117 669 Planarity : 0.004 0.051 762 Dihedral : 7.078 55.649 601 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.28 % Allowed : 21.13 % 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: 0.16 (0.35), residues: 546 helix: 0.66 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.02 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 174 PHE 0.015 0.002 PHE I 152 TYR 0.012 0.001 TYR I 130 ARG 0.007 0.001 ARG I 440 *********************** 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 129 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7596 (mtp85) cc_final: 0.7332 (ttt-90) REVERT: I 346 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: I 386 MET cc_start: 0.8751 (ttm) cc_final: 0.8431 (ttm) REVERT: I 438 LYS cc_start: 0.8541 (tttt) cc_final: 0.8298 (ttpt) REVERT: J 97 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5843 (pm20) REVERT: J 170 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7659 (mt) REVERT: J 337 MET cc_start: 0.6817 (mmt) cc_final: 0.6605 (mmt) outliers start: 31 outliers final: 24 residues processed: 121 average time/residue: 0.2194 time to fit residues: 31.6629 Evaluate side-chains 119 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 153 VAL 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 360 THR 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 97 GLU Chi-restraints excluded: chain J residue 151 ASP 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 287 LEU 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: 0.5980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 201 GLN J 235 GLN J 264 GLN J 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4382 Z= 0.183 Angle : 0.500 6.273 5914 Z= 0.271 Chirality : 0.037 0.117 669 Planarity : 0.004 0.051 762 Dihedral : 6.885 58.569 601 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.34 % Allowed : 22.77 % 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: 0.48 (0.35), residues: 546 helix: 0.91 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.89 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.001 0.000 HIS J 174 PHE 0.014 0.001 PHE I 367 TYR 0.014 0.001 TYR I 130 ARG 0.006 0.001 ARG I 440 *********************** 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 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7472 (m-30) cc_final: 0.7121 (t0) REVERT: I 346 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: I 381 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8050 (mp) REVERT: I 386 MET cc_start: 0.8759 (ttm) cc_final: 0.8434 (ttm) REVERT: I 438 LYS cc_start: 0.8537 (tttt) cc_final: 0.8290 (ttpt) REVERT: J 86 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7157 (mmt-90) REVERT: J 97 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6030 (pm20) REVERT: J 170 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7650 (mt) REVERT: J 265 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6652 (mt-10) REVERT: J 337 MET cc_start: 0.6743 (mmt) cc_final: 0.6457 (mmt) outliers start: 27 outliers final: 17 residues processed: 113 average time/residue: 0.2236 time to fit residues: 30.0932 Evaluate side-chains 116 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 306 ASP 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 360 THR 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 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 198 PHE Chi-restraints excluded: chain J residue 287 LEU 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4382 Z= 0.216 Angle : 0.520 8.226 5914 Z= 0.281 Chirality : 0.037 0.113 669 Planarity : 0.004 0.052 762 Dihedral : 6.509 56.867 599 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.81 % Allowed : 22.30 % 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: 0.51 (0.35), residues: 546 helix: 0.93 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.000 HIS J 327 PHE 0.015 0.001 PHE I 367 TYR 0.006 0.001 TYR J 249 ARG 0.006 0.001 ARG I 440 *********************** 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 126 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7484 (m-30) cc_final: 0.7134 (t0) REVERT: I 381 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8021 (mp) REVERT: I 386 MET cc_start: 0.8691 (ttm) cc_final: 0.8344 (ttm) REVERT: J 86 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7051 (mmt-90) REVERT: J 97 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5943 (pm20) REVERT: J 170 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7663 (mt) REVERT: J 265 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6797 (mt-10) REVERT: J 337 MET cc_start: 0.6754 (mmt) cc_final: 0.6512 (mmt) outliers start: 29 outliers final: 22 residues processed: 119 average time/residue: 0.2179 time to fit residues: 30.8273 Evaluate side-chains 120 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 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 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 360 THR 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 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 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: 0.6980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7357 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4382 Z= 0.208 Angle : 0.521 8.981 5914 Z= 0.279 Chirality : 0.037 0.114 669 Planarity : 0.004 0.051 762 Dihedral : 6.440 57.193 599 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 7.75 % Allowed : 21.13 % Favored : 71.13 % 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: 0.59 (0.35), residues: 546 helix: 1.01 (0.27), residues: 378 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.002 0.000 HIS J 327 PHE 0.014 0.001 PHE I 367 TYR 0.005 0.001 TYR J 163 ARG 0.005 0.001 ARG I 347 *********************** 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 129 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 96 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7476 (m-30) cc_final: 0.7120 (t0) REVERT: I 346 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: I 381 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8026 (mp) REVERT: I 386 MET cc_start: 0.8696 (ttm) cc_final: 0.8341 (ttm) REVERT: J 86 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7040 (mmt-90) REVERT: J 97 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: J 170 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7658 (mt) REVERT: J 265 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6673 (mt-10) REVERT: J 337 MET cc_start: 0.6681 (mmt) cc_final: 0.6445 (mmt) REVERT: J 367 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8155 (mm) outliers start: 33 outliers final: 26 residues processed: 121 average time/residue: 0.2228 time to fit residues: 32.0540 Evaluate side-chains 125 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 MET 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 346 GLN Chi-restraints excluded: chain I residue 360 THR 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 151 ASP 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 287 LEU 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: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4382 Z= 0.301 Angle : 0.615 9.343 5914 Z= 0.328 Chirality : 0.039 0.115 669 Planarity : 0.004 0.052 762 Dihedral : 6.771 57.109 599 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 8.22 % Allowed : 22.77 % Favored : 69.01 % 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: 0.84 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 165 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 J 289 TYR 0.007 0.001 TYR I 334 ARG 0.009 0.001 ARG I 440 *********************** 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 129 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7526 (m-30) cc_final: 0.7167 (t0) REVERT: I 346 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: I 386 MET cc_start: 0.8698 (ttm) cc_final: 0.8385 (ttm) REVERT: J 86 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7155 (mmt-90) REVERT: J 97 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: J 170 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7645 (mt) REVERT: J 337 MET cc_start: 0.6688 (mmt) cc_final: 0.6430 (mmt) REVERT: J 367 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8179 (mm) outliers start: 35 outliers final: 28 residues processed: 119 average time/residue: 0.2115 time to fit residues: 30.0491 Evaluate side-chains 126 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 153 VAL 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 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 151 ASP 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 287 LEU Chi-restraints excluded: chain J residue 288 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4382 Z= 0.240 Angle : 0.594 9.469 5914 Z= 0.315 Chirality : 0.038 0.119 669 Planarity : 0.004 0.051 762 Dihedral : 6.608 57.443 599 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 7.51 % Allowed : 23.47 % Favored : 69.01 % 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: 0.87 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.84 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS J 327 PHE 0.015 0.001 PHE I 367 TYR 0.006 0.001 TYR I 334 ARG 0.009 0.001 ARG I 440 *********************** 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 126 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7530 (m-30) cc_final: 0.7144 (t0) REVERT: I 346 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: I 381 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7991 (mp) REVERT: I 386 MET cc_start: 0.8691 (ttm) cc_final: 0.8370 (ttm) REVERT: J 97 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: J 170 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7635 (mt) REVERT: J 337 MET cc_start: 0.6630 (mmt) cc_final: 0.6366 (mmt) REVERT: J 367 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8184 (mm) outliers start: 32 outliers final: 23 residues processed: 115 average time/residue: 0.2241 time to fit residues: 30.5764 Evaluate side-chains 122 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 MET 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 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 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 151 ASP 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 287 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 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: 0.7377 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4382 Z= 0.251 Angle : 0.594 9.820 5914 Z= 0.315 Chirality : 0.038 0.116 669 Planarity : 0.004 0.052 762 Dihedral : 6.257 57.300 595 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.81 % Allowed : 24.18 % Favored : 69.01 % 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: 0.52 (0.35), residues: 546 helix: 0.90 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.83 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 PHE 0.016 0.001 PHE I 367 TYR 0.006 0.001 TYR I 334 ARG 0.009 0.001 ARG I 440 ********************** 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 121 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.7535 (m-30) cc_final: 0.7160 (t0) REVERT: I 325 ARG cc_start: 0.6742 (ttm-80) cc_final: 0.6451 (tpp-160) REVERT: I 346 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7879 (tm130) REVERT: I 381 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8001 (mp) REVERT: I 386 MET cc_start: 0.8735 (ttm) cc_final: 0.8375 (ttm) REVERT: J 97 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6077 (pm20) REVERT: J 170 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7641 (mt) REVERT: J 265 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6789 (mt-10) REVERT: J 337 MET cc_start: 0.6632 (mmt) cc_final: 0.6370 (mmt) REVERT: J 367 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (mm) outliers start: 29 outliers final: 24 residues processed: 113 average time/residue: 0.2216 time to fit residues: 29.9451 Evaluate side-chains 119 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 147 MET 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 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 94 SER Chi-restraints excluded: chain J residue 97 GLU Chi-restraints excluded: chain J residue 151 ASP 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 287 LEU Chi-restraints excluded: chain J residue 288 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0020 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.3346 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.147292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125731 restraints weight = 7177.877| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.54 r_work: 0.3592 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3579 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 : 0.571 9.707 5914 Z= 0.300 Chirality : 0.036 0.130 669 Planarity : 0.004 0.051 762 Dihedral : 6.002 57.594 595 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.57 % Allowed : 24.88 % Favored : 68.54 % 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: 0.67 (0.35), residues: 546 helix: 1.01 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.75 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.001 0.000 HIS J 98 PHE 0.013 0.001 PHE I 367 TYR 0.007 0.001 TYR I 334 ARG 0.008 0.001 ARG I 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.41 seconds wall clock time: 26 minutes 20.19 seconds (1580.19 seconds total)