Starting phenix.real_space_refine on Wed Jul 23 21:08:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqo_22291/07_2025/6xqo_22291.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqo_22291/07_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_22291/07_2025/6xqo_22291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqo_22291/07_2025/6xqo_22291.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqo_22291/07_2025/6xqo_22291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqo_22291/07_2025/6xqo_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-5711/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: 3.34, per 1000 atoms: 0.78 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 503.0 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: 0.48 Creating SS restraints... Processing helix chain 'I' and resid 110 through 121 Processing helix chain 'I' and resid 123 through 132 Processing helix chain 'I' and resid 148 through 155 removed outlier: 3.555A pdb=" N PHE I 152 " --> pdb=" O THR I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 removed outlier: 3.690A pdb=" N THR I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 217 Processing helix chain 'I' and resid 219 through 231 removed outlier: 3.939A pdb=" N ILE I 225 " --> pdb=" O ARG I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 252 removed outlier: 3.753A pdb=" N PHE I 243 " --> pdb=" O ASP I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 283 Processing helix chain 'I' and resid 292 through 314 removed outlier: 3.505A pdb=" N PHE I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU I 310 " --> pdb=" O ASP I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 339 through 353 removed outlier: 4.304A pdb=" N LYS I 350 " --> pdb=" O GLN I 346 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS I 351 " --> pdb=" O ARG I 347 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE I 353 " --> pdb=" O LEU I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 373 removed outlier: 3.665A pdb=" N VAL I 364 " --> pdb=" O THR I 360 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN I 373 " --> pdb=" O THR I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 381 removed outlier: 3.756A pdb=" N THR I 379 " --> pdb=" O ASN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 387 Processing helix chain 'I' and resid 392 through 404 Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.611A pdb=" N CYS I 413 " --> pdb=" O SER I 409 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP I 421 " --> pdb=" O PHE I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.930A pdb=" N LEU I 441 " --> pdb=" O MET I 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 94 Processing helix chain 'J' and resid 105 through 115 removed outlier: 3.602A pdb=" N PHE J 111 " --> pdb=" O ARG J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 142 removed outlier: 4.160A pdb=" N ILE J 139 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA J 142 " --> pdb=" O GLY J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.140A pdb=" N THR J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 175 through 185 removed outlier: 4.702A pdb=" N VAL J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 211 removed outlier: 3.530A pdb=" N PHE J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS J 199 " --> pdb=" O ARG J 195 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU J 200 " --> pdb=" O GLU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 239 Processing helix chain 'J' and resid 248 through 272 Processing helix chain 'J' and resid 280 through 291 Processing helix chain 'J' and resid 296 through 306 removed outlier: 4.190A pdb=" N TRP J 300 " --> pdb=" O LYS J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 removed outlier: 3.599A pdb=" N PHE J 318 " --> pdb=" O SER J 314 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS J 327 " --> pdb=" O HIS J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 342 removed outlier: 5.258A pdb=" N MET J 337 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N PHE J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA J 341 " --> pdb=" O MET J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 358 Processing helix chain 'J' and resid 363 through 374 removed outlier: 3.597A pdb=" N LEU J 367 " --> pdb=" O SER J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 392 removed outlier: 4.021A pdb=" N GLY J 389 " --> pdb=" O GLU J 385 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL J 390 " --> pdb=" O GLU J 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 134 through 135 Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'J' and resid 278 through 279 249 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.25 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: 1.990 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14693 ( 249) hydrogen bonds : angle 6.31334 ( 735) covalent geometry : bond 0.00419 ( 4382) covalent geometry : angle 0.57272 ( 5914) *********************** 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 : 0.524 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: 0.2504 time to fit residues: 38.2337 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 : 0.515 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124839 restraints weight = 7406.370| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.35 r_work: 0.3612 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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= 0.172 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 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 249) hydrogen bonds : angle 4.32315 ( 735) covalent geometry : bond 0.00402 ( 4382) covalent geometry : angle 0.55980 ( 5914) *********************** 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 : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 437 MET cc_start: 0.8719 (mmt) cc_final: 0.8354 (mmt) REVERT: I 438 LYS cc_start: 0.8653 (tttt) cc_final: 0.8451 (ttpt) REVERT: J 97 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6428 (pm20) REVERT: J 102 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: J 118 MET cc_start: 0.5840 (pp-130) cc_final: 0.5544 (pp-130) REVERT: J 170 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7898 (mt) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.2166 time to fit residues: 34.5924 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 : 0.471 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 39 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.148393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128764 restraints weight = 7301.071| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.35 r_work: 0.3650 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2690 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= 0.117 Angle : 0.479 5.465 5914 Z= 0.264 Chirality : 0.036 0.113 669 Planarity : 0.004 0.049 762 Dihedral : 6.816 54.675 601 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.40 % Allowed : 19.48 % Favored : 75.12 % 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: -0.04 (0.34), residues: 546 helix: 0.55 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 286 HIS 0.002 0.001 HIS J 178 PHE 0.014 0.001 PHE I 367 TYR 0.014 0.001 TYR I 130 ARG 0.005 0.001 ARG I 301 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 249) hydrogen bonds : angle 3.91502 ( 735) covalent geometry : bond 0.00267 ( 4382) covalent geometry : angle 0.47933 ( 5914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 381 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8304 (mp) REVERT: I 386 MET cc_start: 0.8720 (ttm) cc_final: 0.8467 (ttm) REVERT: I 437 MET cc_start: 0.8611 (mmt) cc_final: 0.8407 (mmt) REVERT: I 438 LYS cc_start: 0.8684 (tttt) cc_final: 0.8457 (ttpt) REVERT: J 86 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7337 (mmt-90) REVERT: J 97 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6486 (pm20) REVERT: J 170 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7955 (mt) REVERT: J 201 GLN cc_start: 0.8203 (mm110) cc_final: 0.7383 (mt0) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.2149 time to fit residues: 32.1572 Evaluate side-chains 115 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 39 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.0470 chunk 38 optimal weight: 0.5980 overall best weight: 0.2396 ------------------------------------------------------------------------------- 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 264 GLN J 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.148687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127277 restraints weight = 7140.419| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.55 r_work: 0.3614 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4382 Z= 0.106 Angle : 0.476 5.465 5914 Z= 0.258 Chirality : 0.036 0.124 669 Planarity : 0.004 0.049 762 Dihedral : 6.631 57.622 601 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.87 % Allowed : 22.07 % Favored : 72.07 % 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: 0.46 (0.35), residues: 546 helix: 0.92 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 286 HIS 0.001 0.000 HIS J 174 PHE 0.013 0.001 PHE J 289 TYR 0.014 0.001 TYR I 130 ARG 0.005 0.001 ARG I 301 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 249) hydrogen bonds : angle 3.80214 ( 735) covalent geometry : bond 0.00237 ( 4382) covalent geometry : angle 0.47570 ( 5914) *********************** 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 128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 346 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: I 381 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8098 (mp) REVERT: I 386 MET cc_start: 0.8892 (ttm) cc_final: 0.8572 (ttm) REVERT: I 438 LYS cc_start: 0.8515 (tttt) cc_final: 0.8233 (ttpt) REVERT: J 86 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7377 (mmt-90) REVERT: J 97 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: J 170 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7844 (mt) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 0.2312 time to fit residues: 32.5560 Evaluate side-chains 114 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 235 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 = 0.145690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.123910 restraints weight = 7304.175| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.57 r_work: 0.3566 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4382 Z= 0.154 Angle : 0.531 6.897 5914 Z= 0.290 Chirality : 0.038 0.111 669 Planarity : 0.004 0.050 762 Dihedral : 6.244 56.575 597 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.57 % Allowed : 22.07 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.35), residues: 546 helix: 0.93 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.81 (0.43), residues: 171 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 0.014 0.001 PHE I 367 TYR 0.006 0.001 TYR J 102 ARG 0.008 0.001 ARG I 440 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 249) hydrogen bonds : angle 3.96455 ( 735) covalent geometry : bond 0.00364 ( 4382) covalent geometry : angle 0.53133 ( 5914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 346 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: I 381 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8085 (mp) REVERT: I 386 MET cc_start: 0.8888 (ttm) cc_final: 0.8540 (ttm) REVERT: I 438 LYS cc_start: 0.8515 (tttt) cc_final: 0.8279 (ttpt) REVERT: J 86 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7367 (mmt-90) REVERT: J 97 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: J 170 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7764 (mt) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.2277 time to fit residues: 31.8621 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 : 0.468 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.145225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.123379 restraints weight = 7271.889| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.55 r_work: 0.3560 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 0.031 4382 Z= 0.164 Angle : 0.535 8.526 5914 Z= 0.291 Chirality : 0.038 0.114 669 Planarity : 0.004 0.051 762 Dihedral : 6.368 57.085 597 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.81 % Allowed : 21.13 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.35), residues: 546 helix: 0.89 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.87 (0.43), residues: 165 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 0.001 PHE I 367 TYR 0.006 0.001 TYR J 102 ARG 0.007 0.001 ARG I 440 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 249) hydrogen bonds : angle 4.00907 ( 735) covalent geometry : bond 0.00388 ( 4382) covalent geometry : angle 0.53543 ( 5914) *********************** 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 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 346 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: I 381 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8097 (mp) REVERT: I 386 MET cc_start: 0.8801 (ttm) cc_final: 0.8475 (ttm) REVERT: I 438 LYS cc_start: 0.8532 (tttt) cc_final: 0.8301 (ttpt) REVERT: J 97 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5986 (pm20) REVERT: J 170 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7744 (mt) REVERT: J 236 MET cc_start: 0.6192 (mmp) cc_final: 0.5758 (mmp) REVERT: J 337 MET cc_start: 0.6836 (mmt) cc_final: 0.6574 (mmt) outliers start: 29 outliers final: 22 residues processed: 118 average time/residue: 0.2166 time to fit residues: 30.4847 Evaluate side-chains 116 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 19 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 = 0.3946 r_free = 0.3946 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123284 restraints weight = 7195.158| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.50 r_work: 0.3562 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4382 Z= 0.173 Angle : 0.585 8.861 5914 Z= 0.314 Chirality : 0.039 0.114 669 Planarity : 0.004 0.052 762 Dihedral : 5.961 57.134 593 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 7.04 % Allowed : 21.83 % 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: 0.50 (0.35), residues: 546 helix: 0.90 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -0.87 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 300 HIS 0.002 0.001 HIS J 327 PHE 0.015 0.002 PHE J 289 TYR 0.006 0.001 TYR I 334 ARG 0.007 0.001 ARG I 440 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 249) hydrogen bonds : angle 4.04310 ( 735) covalent geometry : bond 0.00410 ( 4382) covalent geometry : angle 0.58478 ( 5914) *********************** 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 119 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.8043 (m-30) cc_final: 0.7404 (t0) REVERT: I 346 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: I 381 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8113 (mp) REVERT: I 386 MET cc_start: 0.8821 (ttm) cc_final: 0.8453 (ttm) REVERT: I 438 LYS cc_start: 0.8552 (tttt) cc_final: 0.8338 (ttpt) REVERT: J 97 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6024 (pm20) REVERT: J 170 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7774 (mt) REVERT: J 236 MET cc_start: 0.6236 (mmp) cc_final: 0.5752 (mmp) REVERT: J 337 MET cc_start: 0.6842 (mmt) cc_final: 0.6532 (mmt) outliers start: 30 outliers final: 23 residues processed: 111 average time/residue: 0.2146 time to fit residues: 28.5702 Evaluate side-chains 117 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 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 = 0.3948 r_free = 0.3948 target = 0.144938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.123512 restraints weight = 7090.757| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.51 r_work: 0.3566 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3263 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= 0.159 Angle : 0.577 9.269 5914 Z= 0.305 Chirality : 0.038 0.113 669 Planarity : 0.004 0.051 762 Dihedral : 5.887 57.178 593 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.81 % Allowed : 22.77 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 546 helix: 0.95 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.89 (0.42), 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 174 PHE 0.016 0.001 PHE J 289 TYR 0.007 0.001 TYR I 334 ARG 0.009 0.001 ARG I 347 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 249) hydrogen bonds : angle 3.97847 ( 735) covalent geometry : bond 0.00378 ( 4382) covalent geometry : angle 0.57729 ( 5914) *********************** 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 120 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.8096 (m-30) cc_final: 0.7441 (t0) REVERT: I 325 ARG cc_start: 0.7462 (ttm110) cc_final: 0.7173 (ttm-80) REVERT: I 346 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: I 381 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8118 (mp) REVERT: I 386 MET cc_start: 0.8830 (ttm) cc_final: 0.8453 (ttm) REVERT: I 438 LYS cc_start: 0.8538 (tttt) cc_final: 0.8318 (ttpt) REVERT: J 97 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: J 170 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7752 (mt) REVERT: J 236 MET cc_start: 0.6129 (mmp) cc_final: 0.5614 (mmp) REVERT: J 337 MET cc_start: 0.6771 (mmt) cc_final: 0.6475 (mmt) outliers start: 29 outliers final: 24 residues processed: 111 average time/residue: 0.2159 time to fit residues: 28.6968 Evaluate side-chains 117 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 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 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 49 optimal weight: 0.3980 chunk 47 optimal weight: 0.0060 chunk 20 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.146885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125488 restraints weight = 7170.450| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.54 r_work: 0.3589 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3522 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= 0.127 Angle : 0.554 9.418 5914 Z= 0.291 Chirality : 0.036 0.130 669 Planarity : 0.004 0.050 762 Dihedral : 5.683 57.206 593 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.34 % Allowed : 24.18 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.35), residues: 546 helix: 1.12 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.75 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.001 0.000 HIS I 315 PHE 0.020 0.001 PHE J 387 TYR 0.006 0.001 TYR I 334 ARG 0.009 0.001 ARG I 347 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 249) hydrogen bonds : angle 3.84460 ( 735) covalent geometry : bond 0.00299 ( 4382) covalent geometry : angle 0.55396 ( 5914) *********************** 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 125 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.8046 (m-30) cc_final: 0.7385 (t0) REVERT: I 325 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7103 (ttm-80) REVERT: I 346 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: I 381 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8151 (mp) REVERT: I 386 MET cc_start: 0.8869 (ttm) cc_final: 0.8474 (ttm) REVERT: I 438 LYS cc_start: 0.8538 (tttt) cc_final: 0.8311 (ttpt) REVERT: J 97 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6237 (pm20) REVERT: J 170 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7770 (mt) REVERT: J 172 LYS cc_start: 0.8518 (tptt) cc_final: 0.8102 (mptt) REVERT: J 337 MET cc_start: 0.6702 (mmt) cc_final: 0.6393 (mmt) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.2230 time to fit residues: 31.2952 Evaluate side-chains 113 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.146431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124940 restraints weight = 7072.900| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.50 r_work: 0.3570 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3507 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= 0.139 Angle : 0.578 9.707 5914 Z= 0.303 Chirality : 0.037 0.127 669 Planarity : 0.004 0.051 762 Dihedral : 5.711 56.994 593 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.63 % Allowed : 24.88 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.35), residues: 546 helix: 1.15 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 300 HIS 0.001 0.001 HIS J 174 PHE 0.021 0.001 PHE J 387 TYR 0.006 0.001 TYR I 334 ARG 0.008 0.001 ARG I 347 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 249) hydrogen bonds : angle 3.89763 ( 735) covalent geometry : bond 0.00332 ( 4382) covalent geometry : angle 0.57836 ( 5914) ********************** 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 112 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 319 ASP cc_start: 0.8064 (m-30) cc_final: 0.7399 (t0) REVERT: I 325 ARG cc_start: 0.7396 (ttm110) cc_final: 0.7075 (ttm-80) REVERT: I 346 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: I 381 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8132 (mp) REVERT: I 386 MET cc_start: 0.8878 (ttm) cc_final: 0.8485 (ttm) REVERT: I 438 LYS cc_start: 0.8518 (tttt) cc_final: 0.8316 (ttpt) REVERT: J 97 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6201 (pm20) REVERT: J 170 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7764 (mt) REVERT: J 337 MET cc_start: 0.6758 (mmt) cc_final: 0.6454 (mmt) outliers start: 24 outliers final: 20 residues processed: 106 average time/residue: 0.2233 time to fit residues: 28.1462 Evaluate side-chains 111 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.3732 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.147169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125591 restraints weight = 7157.888| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.52 r_work: 0.3592 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3607 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= 0.132 Angle : 0.567 9.594 5914 Z= 0.297 Chirality : 0.037 0.130 669 Planarity : 0.004 0.051 762 Dihedral : 5.652 57.355 593 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.63 % Allowed : 24.65 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.35), residues: 546 helix: 1.19 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.61 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 286 HIS 0.002 0.000 HIS I 315 PHE 0.021 0.001 PHE J 387 TYR 0.006 0.001 TYR I 334 ARG 0.008 0.001 ARG I 347 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 249) hydrogen bonds : angle 3.84822 ( 735) covalent geometry : bond 0.00315 ( 4382) covalent geometry : angle 0.56719 ( 5914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2441.05 seconds wall clock time: 42 minutes 28.44 seconds (2548.44 seconds total)