Starting phenix.real_space_refine on Fri Aug 22 14:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_22291.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_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/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_22291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_22291.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_22291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqo_22291/08_2025/6xqo_22291.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} 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: {'GLU:plan': 10, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1} 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: 1.34, per 1000 atoms: 0.31 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: 0.38 Conformation dependent library (CDL) restraints added in 184.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.14 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: 0.61 Time building geometry restraints manager: 0.52 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- 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= 0.190 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG I 401 TYR 0.010 0.001 TYR J 102 PHE 0.014 0.002 PHE I 367 TRP 0.002 0.001 TRP J 286 HIS 0.003 0.001 HIS J 98 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4382) covalent geometry : angle 0.57272 ( 5914) hydrogen bonds : bond 0.14693 ( 249) hydrogen bonds : angle 6.31334 ( 735) *********************** 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 to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.176 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: 0.1161 time to fit residues: 17.7341 Evaluate side-chains 109 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.144319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.123883 restraints weight = 7450.610| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.41 r_work: 0.3609 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2022 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= 0.166 Angle : 0.554 5.182 5914 Z= 0.304 Chirality : 0.039 0.119 669 Planarity : 0.004 0.041 762 Dihedral : 7.271 52.274 606 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.10 % Allowed : 18.31 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.33), residues: 546 helix: -0.12 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 314 TYR 0.017 0.002 TYR J 249 PHE 0.015 0.002 PHE I 367 TRP 0.003 0.001 TRP J 286 HIS 0.002 0.001 HIS J 174 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4382) covalent geometry : angle 0.55410 ( 5914) hydrogen bonds : bond 0.04528 ( 249) hydrogen bonds : angle 4.33450 ( 735) *********************** 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 to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 437 MET cc_start: 0.8739 (mmt) cc_final: 0.8371 (mmt) REVERT: I 438 LYS cc_start: 0.8645 (tttt) cc_final: 0.8431 (ttpt) REVERT: J 97 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: J 102 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: J 118 MET cc_start: 0.5822 (pp-130) cc_final: 0.5528 (pp-130) REVERT: J 170 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7952 (mt) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.0977 time to fit residues: 15.4717 Evaluate side-chains 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.146482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.124769 restraints weight = 7252.122| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.61 r_work: 0.3582 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4382 Z= 0.124 Angle : 0.486 5.376 5914 Z= 0.268 Chirality : 0.037 0.112 669 Planarity : 0.004 0.048 762 Dihedral : 6.855 53.856 601 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.16 % Allowed : 20.42 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.34), residues: 546 helix: 0.53 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.22 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 440 TYR 0.014 0.001 TYR I 130 PHE 0.015 0.001 PHE I 367 TRP 0.003 0.001 TRP J 286 HIS 0.002 0.001 HIS J 178 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4382) covalent geometry : angle 0.48591 ( 5914) hydrogen bonds : bond 0.03675 ( 249) hydrogen bonds : angle 3.96293 ( 735) *********************** 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 to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 381 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8066 (mp) REVERT: I 386 MET cc_start: 0.8890 (ttm) cc_final: 0.8592 (ttm) REVERT: I 437 MET cc_start: 0.8828 (mmt) cc_final: 0.8625 (mmt) REVERT: I 438 LYS cc_start: 0.8531 (tttt) cc_final: 0.8205 (ttpt) REVERT: J 86 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7219 (mmt-90) REVERT: J 97 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6071 (pm20) REVERT: J 170 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7848 (mt) REVERT: J 265 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7262 (mt-10) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.1070 time to fit residues: 15.8827 Evaluate side-chains 118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 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 264 GLN J 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.124260 restraints weight = 7197.896| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.44 r_work: 0.3576 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4382 Z= 0.144 Angle : 0.509 5.729 5914 Z= 0.280 Chirality : 0.038 0.112 669 Planarity : 0.004 0.051 762 Dihedral : 6.899 55.217 601 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 6.57 % Allowed : 22.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.35), residues: 546 helix: 0.73 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 440 TYR 0.013 0.001 TYR I 130 PHE 0.015 0.001 PHE I 367 TRP 0.002 0.001 TRP J 286 HIS 0.002 0.001 HIS J 174 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4382) covalent geometry : angle 0.50945 ( 5914) hydrogen bonds : bond 0.03883 ( 249) hydrogen bonds : angle 4.01383 ( 735) *********************** 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 124 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 346 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: I 381 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8109 (mp) REVERT: I 386 MET cc_start: 0.8913 (ttm) cc_final: 0.8607 (ttm) REVERT: I 437 MET cc_start: 0.8839 (mmt) cc_final: 0.8632 (mmt) REVERT: I 438 LYS cc_start: 0.8547 (tttt) cc_final: 0.8284 (ttpt) REVERT: J 86 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7356 (mmt-90) REVERT: J 97 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6085 (pm20) REVERT: J 170 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7820 (mt) REVERT: J 337 MET cc_start: 0.6799 (mmt) cc_final: 0.6538 (mmt) outliers start: 28 outliers final: 21 residues processed: 116 average time/residue: 0.1052 time to fit residues: 14.4883 Evaluate side-chains 119 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 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 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 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 51 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.123793 restraints weight = 7207.442| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.49 r_work: 0.3564 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4382 Z= 0.155 Angle : 0.528 6.181 5914 Z= 0.288 Chirality : 0.038 0.113 669 Planarity : 0.004 0.052 762 Dihedral : 6.992 56.179 601 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 7.28 % Allowed : 21.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.35), residues: 546 helix: 0.84 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 440 TYR 0.014 0.001 TYR I 130 PHE 0.015 0.002 PHE I 367 TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 174 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4382) covalent geometry : angle 0.52751 ( 5914) hydrogen bonds : bond 0.03942 ( 249) hydrogen bonds : angle 4.00656 ( 735) *********************** 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 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7527 (ttt-90) REVERT: I 346 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: I 381 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8128 (mp) REVERT: I 386 MET cc_start: 0.8816 (ttm) cc_final: 0.8492 (ttm) REVERT: I 437 MET cc_start: 0.8859 (mmt) cc_final: 0.8616 (mmt) REVERT: I 438 LYS cc_start: 0.8545 (tttt) cc_final: 0.8287 (ttpt) REVERT: J 86 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7420 (mmt-90) REVERT: J 97 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6099 (pm20) REVERT: J 170 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7786 (mt) REVERT: J 265 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7271 (mt-10) REVERT: J 337 MET cc_start: 0.6848 (mmt) cc_final: 0.6567 (mmt) outliers start: 31 outliers final: 23 residues processed: 119 average time/residue: 0.1008 time to fit residues: 14.2700 Evaluate side-chains 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123264 restraints weight = 7296.512| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2989 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= 0.157 Angle : 0.530 7.848 5914 Z= 0.288 Chirality : 0.038 0.114 669 Planarity : 0.004 0.052 762 Dihedral : 7.013 56.855 601 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.35), residues: 546 helix: 0.86 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 440 TYR 0.015 0.001 TYR I 130 PHE 0.015 0.001 PHE I 367 TRP 0.002 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 4382) covalent geometry : angle 0.53037 ( 5914) hydrogen bonds : bond 0.03947 ( 249) hydrogen bonds : angle 4.02251 ( 735) *********************** 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 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7508 (ttt-90) REVERT: I 319 ASP cc_start: 0.8077 (m-30) cc_final: 0.7368 (t0) REVERT: I 346 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: I 381 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8060 (mp) REVERT: I 386 MET cc_start: 0.8813 (ttm) cc_final: 0.8461 (ttm) REVERT: I 437 MET cc_start: 0.8865 (mmt) cc_final: 0.8627 (mmt) REVERT: I 438 LYS cc_start: 0.8498 (tttt) cc_final: 0.8227 (ttpt) REVERT: J 86 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7122 (mmt-90) REVERT: J 97 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: J 170 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7752 (mt) REVERT: J 337 MET cc_start: 0.6819 (mmt) cc_final: 0.6534 (mmt) outliers start: 32 outliers final: 21 residues processed: 120 average time/residue: 0.0970 time to fit residues: 13.9540 Evaluate side-chains 119 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 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 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 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 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.144036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122271 restraints weight = 7332.294| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.57 r_work: 0.3546 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3070 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= 0.183 Angle : 0.596 8.735 5914 Z= 0.319 Chirality : 0.039 0.116 669 Planarity : 0.004 0.052 762 Dihedral : 7.147 57.066 601 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 7.75 % Allowed : 22.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.35), residues: 546 helix: 0.82 (0.27), residues: 377 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 440 TYR 0.015 0.001 TYR I 130 PHE 0.015 0.002 PHE I 367 TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4382) covalent geometry : angle 0.59596 ( 5914) hydrogen bonds : bond 0.04239 ( 249) hydrogen bonds : angle 4.10825 ( 735) *********************** 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 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7514 (ttt-90) REVERT: I 319 ASP cc_start: 0.8067 (m-30) cc_final: 0.7360 (t0) REVERT: I 345 MET cc_start: 0.7657 (mtt) cc_final: 0.7361 (mtp) REVERT: I 346 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: I 381 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8061 (mp) REVERT: I 386 MET cc_start: 0.8812 (ttm) cc_final: 0.8408 (ttm) REVERT: I 437 MET cc_start: 0.8912 (mmt) cc_final: 0.8596 (mmt) REVERT: I 438 LYS cc_start: 0.8540 (tttt) cc_final: 0.8286 (ttpt) REVERT: J 97 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6072 (pm20) REVERT: J 170 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7774 (mt) REVERT: J 337 MET cc_start: 0.6805 (mmt) cc_final: 0.6508 (mmt) REVERT: J 367 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8281 (mm) outliers start: 33 outliers final: 27 residues processed: 116 average time/residue: 0.1045 time to fit residues: 14.3907 Evaluate side-chains 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.143452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121776 restraints weight = 7268.032| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.55 r_work: 0.3541 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4382 Z= 0.191 Angle : 0.610 9.174 5914 Z= 0.325 Chirality : 0.039 0.116 669 Planarity : 0.004 0.052 762 Dihedral : 7.227 57.163 601 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 7.75 % Allowed : 22.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.35), residues: 546 helix: 0.78 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 440 TYR 0.016 0.001 TYR I 130 PHE 0.015 0.002 PHE I 152 TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 4382) covalent geometry : angle 0.60963 ( 5914) hydrogen bonds : bond 0.04315 ( 249) hydrogen bonds : angle 4.14949 ( 735) *********************** 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 127 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7521 (ttt-90) REVERT: I 319 ASP cc_start: 0.8104 (m-30) cc_final: 0.7379 (t0) REVERT: I 346 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: I 381 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8046 (mp) REVERT: I 386 MET cc_start: 0.8800 (ttm) cc_final: 0.8399 (ttm) REVERT: I 437 MET cc_start: 0.8905 (mmt) cc_final: 0.8554 (mmt) REVERT: I 438 LYS cc_start: 0.8569 (tttt) cc_final: 0.8316 (ttpt) REVERT: J 97 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6072 (pm20) REVERT: J 170 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7736 (mt) REVERT: J 337 MET cc_start: 0.6809 (mmt) cc_final: 0.6519 (mmt) REVERT: J 367 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8280 (mm) outliers start: 33 outliers final: 27 residues processed: 115 average time/residue: 0.1063 time to fit residues: 14.4908 Evaluate side-chains 123 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 204 ILE 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 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 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122248 restraints weight = 7368.095| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.57 r_work: 0.3544 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4382 Z= 0.176 Angle : 0.617 9.292 5914 Z= 0.325 Chirality : 0.039 0.114 669 Planarity : 0.004 0.051 762 Dihedral : 7.149 57.274 601 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.75 % Allowed : 22.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.35), residues: 546 helix: 0.80 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 440 TYR 0.018 0.001 TYR I 130 PHE 0.017 0.002 PHE J 289 TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 4382) covalent geometry : angle 0.61694 ( 5914) hydrogen bonds : bond 0.04152 ( 249) hydrogen bonds : angle 4.08927 ( 735) *********************** 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 127 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7807 (mtp85) cc_final: 0.7537 (ttt-90) REVERT: I 319 ASP cc_start: 0.8094 (m-30) cc_final: 0.7395 (t0) REVERT: I 381 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8031 (mp) REVERT: I 386 MET cc_start: 0.8802 (ttm) cc_final: 0.8388 (ttm) REVERT: I 437 MET cc_start: 0.8888 (mmt) cc_final: 0.8587 (mmt) REVERT: I 438 LYS cc_start: 0.8542 (tttt) cc_final: 0.8285 (ttpt) REVERT: J 97 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6094 (pm20) REVERT: J 170 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7771 (mt) REVERT: J 337 MET cc_start: 0.6754 (mmt) cc_final: 0.6449 (mmt) REVERT: J 367 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8290 (mm) outliers start: 33 outliers final: 26 residues processed: 117 average time/residue: 0.1025 time to fit residues: 14.2450 Evaluate side-chains 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121897 restraints weight = 7306.771| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.56 r_work: 0.3540 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4382 Z= 0.190 Angle : 0.619 9.592 5914 Z= 0.328 Chirality : 0.040 0.116 669 Planarity : 0.004 0.051 762 Dihedral : 7.214 57.342 601 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.28 % Allowed : 23.94 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.35), residues: 546 helix: 0.77 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 347 TYR 0.018 0.002 TYR I 130 PHE 0.016 0.002 PHE I 152 TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 4382) covalent geometry : angle 0.61855 ( 5914) hydrogen bonds : bond 0.04311 ( 249) hydrogen bonds : angle 4.15900 ( 735) ********************** 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 122 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 154 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7526 (ttt-90) REVERT: I 319 ASP cc_start: 0.8070 (m-30) cc_final: 0.7422 (t0) REVERT: I 381 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8081 (mp) REVERT: I 386 MET cc_start: 0.8794 (ttm) cc_final: 0.8392 (ttm) REVERT: I 437 MET cc_start: 0.8890 (mmt) cc_final: 0.8566 (mmt) REVERT: I 438 LYS cc_start: 0.8584 (tttt) cc_final: 0.8330 (ttpt) REVERT: J 97 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: J 170 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7755 (mt) REVERT: J 337 MET cc_start: 0.6792 (mmt) cc_final: 0.6486 (mmt) REVERT: J 367 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (mm) outliers start: 31 outliers final: 26 residues processed: 113 average time/residue: 0.1043 time to fit residues: 13.9692 Evaluate side-chains 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.144095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.122290 restraints weight = 7373.046| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.60 r_work: 0.3544 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3297 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= 0.171 Angle : 0.607 9.412 5914 Z= 0.321 Chirality : 0.039 0.122 669 Planarity : 0.004 0.052 762 Dihedral : 7.145 57.455 601 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.04 % Allowed : 23.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.35), residues: 546 helix: 0.83 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 440 TYR 0.010 0.001 TYR I 130 PHE 0.018 0.002 PHE J 289 TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4382) covalent geometry : angle 0.60746 ( 5914) hydrogen bonds : bond 0.04091 ( 249) hydrogen bonds : angle 4.08138 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1290.31 seconds wall clock time: 22 minutes 51.70 seconds (1371.70 seconds total)