Starting phenix.real_space_refine on Sun Aug 24 02:18:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psq_17860/08_2025/8psq_17860.map" } resolution = 2.65 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= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 28 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 5032 2.51 5 N 1457 2.21 5 O 1618 1.98 5 H 7898 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 16079 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5030 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 18, 'TRANS': 296} Chain: "B" Number of atoms: 7973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Chain: "C" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2221 Classifications: {'peptide': 139} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "V" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 386 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 466 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 961 SG CYS A 161 48.028 44.792 80.976 1.00 33.76 S ATOM 2850 SG CYS A 282 46.959 47.528 83.512 1.00 39.94 S Time building chain proxies: 3.30, per 1000 atoms: 0.21 Number of scatterers: 16079 At special positions: 0 Unit cell: (88.2, 94.08, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 44 16.00 P 28 15.00 Mg 1 11.99 O 1618 8.00 N 1457 7.00 C 5032 6.00 H 7898 1.00 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: 1.09 Conformation dependent library (CDL) restraints added in 462.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " Number of angles added : 2 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 9 sheets defined 47.6% alpha, 13.0% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.510A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.542A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.923A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.770A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.500A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.678A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.658A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 3.953A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.019A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 498 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.630A pdb=" N LYS C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.700A pdb=" N THR C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.683A pdb=" N SER C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.617A pdb=" N ASP C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 109 removed outlier: 4.148A pdb=" N GLN C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.308A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.308A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'B' and resid 155 through 159 removed outlier: 3.742A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA8, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 83 removed outlier: 9.309A pdb=" N LYS C 73 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N SER C 121 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7876 1.03 - 1.23: 39 1.23 - 1.42: 3518 1.42 - 1.62: 4795 1.62 - 1.81: 64 Bond restraints: 16292 Sorted by residual: bond pdb=" CG1 ILE B 292 " pdb=" CD1 ILE B 292 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.65e-01 bond pdb=" CG PRO A 302 " pdb=" CD PRO A 302 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.33e-01 bond pdb=" CB ASN B 330 " pdb=" CG ASN B 330 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.16e-01 bond pdb=" CB VAL B 357 " pdb=" CG2 VAL B 357 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.15e-01 bond pdb=" N PHE B 287 " pdb=" CA PHE B 287 " ideal model delta sigma weight residual 1.464 1.455 0.009 1.36e-02 5.41e+03 4.11e-01 ... (remaining 16287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 26442 0.87 - 1.74: 2725 1.74 - 2.62: 176 2.62 - 3.49: 64 3.49 - 4.36: 15 Bond angle restraints: 29422 Sorted by residual: angle pdb=" CA VAL B 324 " pdb=" C VAL B 324 " pdb=" N ALA B 325 " ideal model delta sigma weight residual 116.60 119.58 -2.98 1.45e+00 4.76e-01 4.21e+00 angle pdb=" CG LYS C 36 " pdb=" CD LYS C 36 " pdb=" CE LYS C 36 " ideal model delta sigma weight residual 111.30 115.66 -4.36 2.30e+00 1.89e-01 3.59e+00 angle pdb=" N VAL B 324 " pdb=" CA VAL B 324 " pdb=" C VAL B 324 " ideal model delta sigma weight residual 109.34 113.09 -3.75 2.08e+00 2.31e-01 3.25e+00 angle pdb=" CA ARG C 111 " pdb=" CB ARG C 111 " pdb=" CG ARG C 111 " ideal model delta sigma weight residual 114.10 117.34 -3.24 2.00e+00 2.50e-01 2.63e+00 angle pdb=" N GLY A 107 " pdb=" CA GLY A 107 " pdb=" C GLY A 107 " ideal model delta sigma weight residual 115.66 113.15 2.51 1.63e+00 3.76e-01 2.37e+00 ... (remaining 29417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6722 17.67 - 35.34: 621 35.34 - 53.01: 250 53.01 - 70.68: 68 70.68 - 88.36: 23 Dihedral angle restraints: 7684 sinusoidal: 4444 harmonic: 3240 Sorted by residual: dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP B 337 " pdb=" CB ASP B 337 " pdb=" CG ASP B 337 " pdb=" OD1 ASP B 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG B 33 " pdb=" CD ARG B 33 " pdb=" NE ARG B 33 " pdb=" CZ ARG B 33 " ideal model delta sinusoidal sigma weight residual 90.00 44.80 45.20 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 7681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 885 0.028 - 0.057: 312 0.057 - 0.085: 64 0.085 - 0.113: 47 0.113 - 0.141: 14 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA ILE B 125 " pdb=" N ILE B 125 " pdb=" C ILE B 125 " pdb=" CB ILE B 125 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1319 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 470 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 33 " -0.155 9.50e-02 1.11e+02 5.20e-02 3.47e+00 pdb=" NE ARG B 33 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 33 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 33 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 33 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 33 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 33 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 33 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 33 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 501 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO B 502 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " 0.023 5.00e-02 4.00e+02 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1193 2.20 - 2.80: 32246 2.80 - 3.40: 44404 3.40 - 4.00: 60948 4.00 - 4.60: 92406 Nonbonded interactions: 231197 Sorted by model distance: nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.601 2.450 nonbonded pdb=" O2 C V 13 " pdb=" H21 G S 3 " model vdw 1.606 2.450 nonbonded pdb=" OE1 GLU B 72 " pdb=" H GLU B 72 " model vdw 1.621 2.450 nonbonded pdb=" N3 C V 13 " pdb=" H1 G S 3 " model vdw 1.629 2.600 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.641 2.450 ... (remaining 231192 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: 2.310 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.280 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: 0.010 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 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 : 0.003 0.029 8398 Z= 0.119 Angle : 0.471 4.359 11477 Z= 0.252 Chirality : 0.035 0.141 1322 Planarity : 0.004 0.069 1372 Dihedral : 18.195 88.356 3322 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.92 % Rotamer: Outliers : 1.19 % Allowed : 22.43 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.30 (0.28), residues: 963 helix: 1.88 (0.26), residues: 437 sheet: -0.06 (0.47), residues: 101 loop : 0.11 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 33 TYR 0.010 0.001 TYR A 403 PHE 0.016 0.001 PHE C 44 TRP 0.004 0.001 TRP A 346 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8394) covalent geometry : angle 0.47051 (11475) hydrogen bonds : bond 0.12526 ( 389) hydrogen bonds : angle 5.36007 ( 1072) metal coordination : bond 0.00278 ( 4) metal coordination : angle 2.26547 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.442 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 1.5248 time to fit residues: 203.1085 Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 444 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.086071 restraints weight = 24677.999| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.30 r_work: 0.2715 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8398 Z= 0.210 Angle : 0.541 4.625 11477 Z= 0.288 Chirality : 0.039 0.162 1322 Planarity : 0.005 0.048 1372 Dihedral : 12.492 73.317 1488 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.10 % Allowed : 20.29 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.26 (0.27), residues: 963 helix: 1.80 (0.25), residues: 434 sheet: 0.18 (0.48), residues: 95 loop : 0.09 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 68 TYR 0.016 0.002 TYR A 403 PHE 0.023 0.002 PHE C 44 TRP 0.009 0.002 TRP A 346 HIS 0.008 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 8394) covalent geometry : angle 0.54042 (11475) hydrogen bonds : bond 0.06535 ( 389) hydrogen bonds : angle 4.42288 ( 1072) metal coordination : bond 0.00633 ( 4) metal coordination : angle 2.20637 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.439 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 130 average time/residue: 1.6539 time to fit residues: 224.6003 Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.087407 restraints weight = 25054.950| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.36 r_work: 0.2728 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8398 Z= 0.145 Angle : 0.491 4.448 11477 Z= 0.261 Chirality : 0.037 0.150 1322 Planarity : 0.004 0.061 1372 Dihedral : 12.333 73.354 1480 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.39 % Allowed : 20.88 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.36 (0.27), residues: 963 helix: 1.89 (0.25), residues: 434 sheet: 0.23 (0.49), residues: 95 loop : 0.12 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 33 TYR 0.013 0.001 TYR A 403 PHE 0.018 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8394) covalent geometry : angle 0.49050 (11475) hydrogen bonds : bond 0.05916 ( 389) hydrogen bonds : angle 4.23164 ( 1072) metal coordination : bond 0.00388 ( 4) metal coordination : angle 2.15584 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8540 (ttp-110) REVERT: C 93 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7391 (t70) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 1.7296 time to fit residues: 225.8505 Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.086864 restraints weight = 24940.460| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.40 r_work: 0.2760 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8398 Z= 0.124 Angle : 0.473 4.383 11477 Z= 0.250 Chirality : 0.036 0.145 1322 Planarity : 0.004 0.035 1372 Dihedral : 12.260 73.375 1479 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.51 % Allowed : 21.12 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.43 (0.27), residues: 963 helix: 2.01 (0.25), residues: 434 sheet: 0.28 (0.57), residues: 75 loop : 0.10 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.016 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8394) covalent geometry : angle 0.47219 (11475) hydrogen bonds : bond 0.05649 ( 389) hydrogen bonds : angle 4.11578 ( 1072) metal coordination : bond 0.00357 ( 4) metal coordination : angle 2.37684 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 383 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8002 (ttm110) REVERT: B 155 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7770 (mtp85) REVERT: C 93 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7412 (t70) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 1.7904 time to fit residues: 235.5661 Evaluate side-chains 124 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.086777 restraints weight = 24909.889| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.39 r_work: 0.2755 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8398 Z= 0.123 Angle : 0.472 4.369 11477 Z= 0.249 Chirality : 0.036 0.144 1322 Planarity : 0.004 0.069 1372 Dihedral : 12.223 73.338 1479 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.51 % Allowed : 21.48 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.48 (0.27), residues: 963 helix: 2.06 (0.25), residues: 434 sheet: 0.27 (0.58), residues: 75 loop : 0.11 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.015 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8394) covalent geometry : angle 0.47154 (11475) hydrogen bonds : bond 0.05622 ( 389) hydrogen bonds : angle 4.08482 ( 1072) metal coordination : bond 0.00353 ( 4) metal coordination : angle 2.18622 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8353 (t70) cc_final: 0.8050 (t70) REVERT: A 323 ASP cc_start: 0.8149 (p0) cc_final: 0.7922 (p0) REVERT: A 332 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7935 (ttp80) REVERT: A 383 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7925 (ttm110) REVERT: B 155 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7786 (mtp85) REVERT: C 93 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7371 (t70) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 1.7631 time to fit residues: 252.5894 Evaluate side-chains 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.087972 restraints weight = 24849.197| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.39 r_work: 0.2741 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8398 Z= 0.108 Angle : 0.461 4.414 11477 Z= 0.242 Chirality : 0.035 0.142 1322 Planarity : 0.004 0.045 1372 Dihedral : 12.135 73.334 1479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.63 % Allowed : 21.12 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.58 (0.27), residues: 963 helix: 2.18 (0.25), residues: 434 sheet: 0.26 (0.58), residues: 75 loop : 0.13 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8394) covalent geometry : angle 0.45956 (11475) hydrogen bonds : bond 0.05417 ( 389) hydrogen bonds : angle 4.01064 ( 1072) metal coordination : bond 0.00377 ( 4) metal coordination : angle 2.46802 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: A 332 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7955 (ttp80) REVERT: A 383 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7941 (ttm110) REVERT: B 155 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7781 (mtp85) REVERT: C 93 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7365 (t70) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 1.8721 time to fit residues: 252.2066 Evaluate side-chains 131 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 60 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.089676 restraints weight = 24665.221| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.34 r_work: 0.2746 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8398 Z= 0.106 Angle : 0.460 4.305 11477 Z= 0.240 Chirality : 0.035 0.144 1322 Planarity : 0.004 0.041 1372 Dihedral : 12.065 73.310 1479 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.63 % Allowed : 21.12 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.63 (0.27), residues: 963 helix: 2.25 (0.26), residues: 434 sheet: 0.26 (0.57), residues: 75 loop : 0.14 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 33 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8394) covalent geometry : angle 0.45898 (11475) hydrogen bonds : bond 0.05358 ( 389) hydrogen bonds : angle 3.96508 ( 1072) metal coordination : bond 0.00374 ( 4) metal coordination : angle 2.37821 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: A 323 ASP cc_start: 0.8090 (p0) cc_final: 0.7833 (p0) REVERT: A 332 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7939 (ttp80) REVERT: A 383 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7933 (ttm110) REVERT: B 155 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7752 (mtp85) REVERT: C 93 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7281 (t70) outliers start: 22 outliers final: 12 residues processed: 132 average time/residue: 1.8682 time to fit residues: 257.6166 Evaluate side-chains 131 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 155 ARG Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.086700 restraints weight = 24819.052| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.31 r_work: 0.2730 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8398 Z= 0.170 Angle : 0.515 4.455 11477 Z= 0.272 Chirality : 0.038 0.146 1322 Planarity : 0.005 0.086 1372 Dihedral : 12.227 73.255 1479 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.74 % Allowed : 21.36 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.38 (0.27), residues: 963 helix: 1.97 (0.25), residues: 434 sheet: 0.35 (0.58), residues: 73 loop : 0.05 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 33 TYR 0.014 0.001 TYR A 403 PHE 0.022 0.001 PHE C 44 TRP 0.005 0.001 TRP B 426 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8394) covalent geometry : angle 0.51474 (11475) hydrogen bonds : bond 0.06022 ( 389) hydrogen bonds : angle 4.13948 ( 1072) metal coordination : bond 0.00496 ( 4) metal coordination : angle 1.91845 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: A 323 ASP cc_start: 0.8250 (p0) cc_final: 0.8003 (p0) REVERT: A 332 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8042 (ttp80) REVERT: A 383 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8046 (ttm110) REVERT: B 103 THR cc_start: 0.9083 (m) cc_final: 0.8616 (p) REVERT: B 461 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7967 (mpp80) REVERT: C 93 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7310 (t70) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 1.7719 time to fit residues: 237.4992 Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 461 ARG Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN C 28 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.088906 restraints weight = 24726.783| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.31 r_work: 0.2778 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8398 Z= 0.104 Angle : 0.470 4.593 11477 Z= 0.245 Chirality : 0.035 0.144 1322 Planarity : 0.004 0.073 1372 Dihedral : 12.126 73.291 1479 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.27 % Allowed : 21.72 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.58 (0.27), residues: 963 helix: 2.21 (0.25), residues: 434 sheet: 0.06 (0.58), residues: 77 loop : 0.14 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 33 TYR 0.012 0.001 TYR C 95 PHE 0.012 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8394) covalent geometry : angle 0.46927 (11475) hydrogen bonds : bond 0.05415 ( 389) hydrogen bonds : angle 4.00728 ( 1072) metal coordination : bond 0.00343 ( 4) metal coordination : angle 2.45921 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: A 323 ASP cc_start: 0.8085 (p0) cc_final: 0.7842 (p0) REVERT: A 332 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7962 (ttp80) REVERT: A 383 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7981 (ttm110) REVERT: B 103 THR cc_start: 0.9098 (m) cc_final: 0.8717 (p) REVERT: B 461 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7956 (mpp80) REVERT: C 93 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7314 (t70) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 1.7990 time to fit residues: 236.7645 Evaluate side-chains 127 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 461 ARG Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.086500 restraints weight = 24727.158| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.31 r_work: 0.2723 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8398 Z= 0.175 Angle : 0.525 4.469 11477 Z= 0.276 Chirality : 0.038 0.148 1322 Planarity : 0.005 0.074 1372 Dihedral : 12.246 73.243 1479 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 21.84 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.36 (0.27), residues: 963 helix: 1.97 (0.25), residues: 434 sheet: 0.36 (0.59), residues: 73 loop : 0.01 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 33 TYR 0.014 0.001 TYR A 403 PHE 0.022 0.001 PHE C 44 TRP 0.006 0.001 TRP B 426 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8394) covalent geometry : angle 0.52476 (11475) hydrogen bonds : bond 0.06096 ( 389) hydrogen bonds : angle 4.16216 ( 1072) metal coordination : bond 0.00506 ( 4) metal coordination : angle 1.57344 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1926 Ramachandran restraints generated. 963 Oldfield, 0 Emsley, 963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 155 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: A 323 ASP cc_start: 0.8268 (p0) cc_final: 0.8036 (p0) REVERT: A 332 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8074 (ttp80) REVERT: A 383 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8090 (ttm110) REVERT: B 103 THR cc_start: 0.9165 (m) cc_final: 0.8781 (p) REVERT: B 461 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7973 (mpp80) REVERT: C 93 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7287 (t70) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 1.7961 time to fit residues: 232.9441 Evaluate side-chains 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 383 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 461 ARG Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.091135 restraints weight = 24613.426| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.35 r_work: 0.2772 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8398 Z= 0.089 Angle : 0.458 4.552 11477 Z= 0.238 Chirality : 0.035 0.144 1322 Planarity : 0.004 0.069 1372 Dihedral : 12.070 73.324 1479 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.67 % Allowed : 22.43 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.66 (0.28), residues: 963 helix: 2.34 (0.26), residues: 435 sheet: 0.09 (0.58), residues: 77 loop : 0.10 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 33 TYR 0.014 0.001 TYR C 95 PHE 0.006 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 8394) covalent geometry : angle 0.45679 (11475) hydrogen bonds : bond 0.05125 ( 389) hydrogen bonds : angle 3.91752 ( 1072) metal coordination : bond 0.00327 ( 4) metal coordination : angle 3.00434 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6330.60 seconds wall clock time: 107 minutes 53.03 seconds (6473.03 seconds total)