Starting phenix.real_space_refine on Fri Jul 3 21:14:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.cif" model { file = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psq_17860/07_2026/8psq_17860.cif" } 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-dev-6108/lib/python3.11/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: 2.89, per 1000 atoms: 0.18 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: 1.49 Conformation dependent library (CDL) restraints added in 437.9 milliseconds 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: 2.83 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: 3.69 Time building geometry restraints manager: 2.02 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: 6711 17.67 - 35.34: 612 35.34 - 53.01: 237 53.01 - 70.68: 57 70.68 - 88.36: 23 Dihedral angle restraints: 7640 sinusoidal: 4400 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 7637 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: 2.050 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 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 : 17.848 88.356 3286 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 are 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/Z covalent geometry : bond 0.00266 / 0.12 ( 8394) covalent geometry : angle 0.47051 / 0.25 (11475) hydrogen bonds : bond 0.12526 / 8.74 ( 389) hydrogen bonds : angle 5.36007 / 3.67 ( 1072) metal coordination : bond 0.00278 / 0.12 ( 4) metal coordination : angle 2.26547 / 1.23 ( 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 : 0.450 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 127 average time/residue: 1.4653 time to fit residues: 195.9226 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 : 0.443 ------------------------------------------------------------------------------- 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... 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 = 0.3171 r_free = 0.3171 target = 0.109951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.086387 restraints weight = 24646.455| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.34 r_work: 0.2694 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8398 Z= 0.209 Angle : 0.543 4.614 11477 Z= 0.290 Chirality : 0.039 0.162 1322 Planarity : 0.005 0.048 1372 Dihedral : 11.216 73.213 1452 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.58 % Allowed : 19.45 % Favored : 76.97 % 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 are not related in a simple way. whole: 1.25 (0.27), residues: 963 helix: 1.79 (0.25), residues: 434 sheet: 0.19 (0.49), residues: 95 loop : 0.08 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 33 TYR 0.016 0.002 TYR A 403 PHE 0.023 0.002 PHE C 44 TRP 0.010 0.002 TRP A 346 HIS 0.007 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8394) covalent geometry : angle 0.54261 / 0.29 (11475) hydrogen bonds : bond 0.06549 / 4.69 ( 389) hydrogen bonds : angle 4.43137 / 3.12 ( 1072) metal coordination : bond 0.00649 / 0.28 ( 4) metal coordination : angle 2.14074 / 1.17 ( 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 145 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.447 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 134 average time/residue: 1.4325 time to fit residues: 201.9803 Evaluate side-chains 121 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 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: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3164 r_free = 0.3164 target = 0.109532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.085684 restraints weight = 24982.125| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.37 r_work: 0.2716 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8398 Z= 0.191 Angle : 0.526 4.548 11477 Z= 0.281 Chirality : 0.038 0.152 1322 Planarity : 0.005 0.061 1372 Dihedral : 11.141 73.324 1444 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.10 % Allowed : 20.17 % 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 are not related in a simple way. whole: 1.20 (0.27), residues: 963 helix: 1.75 (0.25), residues: 433 sheet: 0.34 (0.50), residues: 93 loop : 0.01 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 33 TYR 0.014 0.001 TYR A 403 PHE 0.022 0.002 PHE C 44 TRP 0.007 0.002 TRP A 346 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 8394) covalent geometry : angle 0.52589 / 0.28 (11475) hydrogen bonds : bond 0.06345 / 4.56 ( 389) hydrogen bonds : angle 4.33185 / 3.08 ( 1072) metal coordination : bond 0.00542 / 0.24 ( 4) metal coordination : angle 1.93399 / 1.05 ( 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 137 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7546 (mmt90) REVERT: B 461 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7895 (tpp80) REVERT: B 513 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8179 (t) REVERT: C 93 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7406 (t70) outliers start: 26 outliers final: 15 residues processed: 125 average time/residue: 1.3672 time to fit residues: 180.2942 Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 103 THR 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 290 ASP Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 406 ASP 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 B residue 513 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 64 optimal weight: 0.0770 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.111992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.088338 restraints weight = 24779.936| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.37 r_work: 0.2736 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.0948 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= 0.112 Angle : 0.466 4.350 11477 Z= 0.246 Chirality : 0.036 0.145 1322 Planarity : 0.004 0.035 1372 Dihedral : 10.985 73.405 1443 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.27 % Allowed : 20.76 % Favored : 76.97 % 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 are not related in a simple way. whole: 1.40 (0.27), residues: 963 helix: 2.01 (0.25), residues: 434 sheet: 0.08 (0.58), residues: 77 loop : 0.10 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 292 TYR 0.011 0.001 TYR A 403 PHE 0.014 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/Z covalent geometry : bond 0.00252 / 0.11 ( 8394) covalent geometry : angle 0.46516 / 0.25 (11475) hydrogen bonds : bond 0.05575 / 4.12 ( 389) hydrogen bonds : angle 4.12906 / 2.95 ( 1072) metal coordination : bond 0.00368 / 0.18 ( 4) metal coordination : angle 2.49966 / 1.35 ( 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 129 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7925 (ttp80) REVERT: B 155 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7802 (mtp85) REVERT: C 93 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7390 (t70) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 1.4332 time to fit residues: 182.2378 Evaluate side-chains 120 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 332 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 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: 1.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3184 r_free = 0.3184 target = 0.111045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.087689 restraints weight = 24789.911| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.31 r_work: 0.2757 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1007 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= 0.121 Angle : 0.470 4.357 11477 Z= 0.248 Chirality : 0.036 0.145 1322 Planarity : 0.004 0.070 1372 Dihedral : 10.945 73.352 1443 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.03 % Allowed : 21.60 % 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 are not related in a simple way. whole: 1.45 (0.27), residues: 963 helix: 2.05 (0.25), residues: 434 sheet: 0.07 (0.58), residues: 77 loop : 0.12 (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 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/Z covalent geometry : bond 0.00276 / 0.12 ( 8394) covalent geometry : angle 0.46939 / 0.25 (11475) hydrogen bonds : bond 0.05617 / 4.14 ( 389) hydrogen bonds : angle 4.08719 / 2.92 ( 1072) metal coordination : bond 0.00345 / 0.17 ( 4) metal coordination : angle 2.28734 / 1.24 ( 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 127 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8550 (mtt) REVERT: A 332 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: A 383 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7952 (ttm110) REVERT: C 93 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7318 (t70) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 1.4615 time to fit residues: 184.3370 Evaluate side-chains 122 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 255 MET 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 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 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.089474 restraints weight = 24697.093| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.37 r_work: 0.2749 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1039 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= 0.098 Angle : 0.449 4.289 11477 Z= 0.236 Chirality : 0.035 0.142 1322 Planarity : 0.004 0.045 1372 Dihedral : 10.823 73.344 1443 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.39 % Allowed : 21.24 % 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 are not related in a simple way. whole: 1.59 (0.28), residues: 963 helix: 2.21 (0.26), residues: 434 sheet: 0.08 (0.58), residues: 77 loop : 0.16 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 33 TYR 0.011 0.001 TYR A 403 PHE 0.012 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/Z covalent geometry : bond 0.00221 / 0.10 ( 8394) covalent geometry : angle 0.44806 / 0.24 (11475) hydrogen bonds : bond 0.05312 / 3.96 ( 389) hydrogen bonds : angle 3.97866 / 2.84 ( 1072) metal coordination : bond 0.00382 / 0.19 ( 4) metal coordination : angle 2.64465 / 1.43 ( 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 139 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8244 (t70) cc_final: 0.7877 (t70) REVERT: A 155 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8075 (tm-30) REVERT: A 332 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: A 383 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7896 (ttm110) REVERT: B 155 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7751 (mtp85) REVERT: C 93 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7315 (t70) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 1.3521 time to fit residues: 185.5519 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 : 0.431 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3191 r_free = 0.3191 target = 0.111569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.087744 restraints weight = 24749.025| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.38 r_work: 0.2731 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1063 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= 0.136 Angle : 0.480 4.390 11477 Z= 0.253 Chirality : 0.036 0.143 1322 Planarity : 0.004 0.042 1372 Dihedral : 10.765 73.353 1443 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.63 % Allowed : 20.53 % Favored : 76.85 % 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 are not related in a simple way. whole: 1.50 (0.27), residues: 963 helix: 2.10 (0.25), residues: 434 sheet: 0.36 (0.58), residues: 73 loop : 0.07 (0.29), residues: 456 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 0.017 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/Z covalent geometry : bond 0.00314 / 0.14 ( 8394) covalent geometry : angle 0.47942 / 0.25 (11475) hydrogen bonds : bond 0.05701 / 4.19 ( 389) hydrogen bonds : angle 4.05771 / 2.90 ( 1072) metal coordination : bond 0.00374 / 0.17 ( 4) metal coordination : angle 2.10435 / 1.14 ( 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 135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8664 (ttmt) REVERT: A 323 ASP cc_start: 0.8166 (p0) cc_final: 0.7902 (p0) REVERT: A 332 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7993 (ttp80) REVERT: A 383 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7975 (ttm110) REVERT: B 461 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7976 (mpp80) REVERT: C 93 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7294 (t70) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 1.3392 time to fit residues: 179.2003 Evaluate side-chains 126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.085561 restraints weight = 24838.644| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.32 r_work: 0.2709 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8398 Z= 0.188 Angle : 0.530 4.492 11477 Z= 0.281 Chirality : 0.038 0.149 1322 Planarity : 0.005 0.087 1372 Dihedral : 10.744 73.451 1443 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.51 % Allowed : 20.88 % 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 are not related in a simple way. whole: 1.26 (0.27), residues: 963 helix: 1.86 (0.25), residues: 434 sheet: 0.35 (0.58), residues: 73 loop : -0.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 33 TYR 0.015 0.001 TYR A 403 PHE 0.023 0.002 PHE C 44 TRP 0.006 0.001 TRP B 426 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 8394) covalent geometry : angle 0.52923 / 0.28 (11475) hydrogen bonds : bond 0.06250 / 4.53 ( 389) hydrogen bonds : angle 4.21112 / 3.00 ( 1072) metal coordination : bond 0.00579 / 0.26 ( 4) metal coordination : angle 1.70094 / 0.93 ( 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 133 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8076 (ttp80) REVERT: A 383 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8061 (ttm110) REVERT: B 461 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7967 (mpp80) REVERT: C 93 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7318 (t70) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 1.5127 time to fit residues: 198.8917 Evaluate side-chains 124 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 357 VAL 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=1.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.110796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.087437 restraints weight = 24738.438| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.32 r_work: 0.2750 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1172 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= 0.136 Angle : 0.492 4.384 11477 Z= 0.260 Chirality : 0.036 0.146 1322 Planarity : 0.004 0.073 1372 Dihedral : 10.630 73.449 1443 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.15 % Allowed : 21.24 % 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 are not related in a simple way. whole: 1.38 (0.27), residues: 963 helix: 2.00 (0.25), residues: 434 sheet: 0.34 (0.58), residues: 73 loop : 0.02 (0.29), residues: 456 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 0.017 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/Z covalent geometry : bond 0.00311 / 0.14 ( 8394) covalent geometry : angle 0.49137 / 0.26 (11475) hydrogen bonds : bond 0.05790 / 4.25 ( 389) hydrogen bonds : angle 4.12264 / 2.95 ( 1072) metal coordination : bond 0.00355 / 0.17 ( 4) metal coordination : angle 2.20122 / 1.19 ( 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 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8186 (p0) cc_final: 0.7911 (p0) REVERT: A 332 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8007 (ttp80) REVERT: A 383 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8011 (ttm110) REVERT: B 461 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7987 (mpp80) REVERT: C 93 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7282 (t70) outliers start: 18 outliers final: 12 residues processed: 123 average time/residue: 1.3950 time to fit residues: 180.2636 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 : 0.430 ------------------------------------------------------------------------------- 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 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 357 VAL 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 30 SER 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: 0.9980 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.109998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.086664 restraints weight = 24674.544| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.31 r_work: 0.2729 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1204 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= 0.167 Angle : 0.516 4.450 11477 Z= 0.273 Chirality : 0.038 0.148 1322 Planarity : 0.005 0.074 1372 Dihedral : 10.684 73.417 1443 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.15 % Allowed : 21.36 % Favored : 76.49 % 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 are not related in a simple way. whole: 1.29 (0.27), residues: 963 helix: 1.90 (0.25), residues: 434 sheet: 0.33 (0.58), 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 0.015 0.001 TYR C 95 PHE 0.020 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/Z covalent geometry : bond 0.00388 / 0.17 ( 8394) covalent geometry : angle 0.51545 / 0.27 (11475) hydrogen bonds : bond 0.06073 / 4.42 ( 389) hydrogen bonds : angle 4.17749 / 2.98 ( 1072) metal coordination : bond 0.00514 / 0.22 ( 4) metal coordination : angle 1.76826 / 0.97 ( 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 130 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8249 (p0) cc_final: 0.7977 (p0) REVERT: A 332 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8013 (ttp80) REVERT: A 383 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8059 (ttm110) REVERT: B 461 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7999 (mpp80) REVERT: C 93 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7290 (t70) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 1.3339 time to fit residues: 172.5265 Evaluate side-chains 128 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 357 VAL 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 30 SER 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: 0.0010 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.0010 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.114459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091250 restraints weight = 24627.625| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.34 r_work: 0.2788 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8398 Z= 0.089 Angle : 0.455 4.555 11477 Z= 0.236 Chirality : 0.035 0.143 1322 Planarity : 0.004 0.068 1372 Dihedral : 10.479 73.495 1443 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.55 % Allowed : 22.08 % 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 are not related in a simple way. whole: 1.64 (0.28), residues: 963 helix: 2.31 (0.26), residues: 435 sheet: 0.12 (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 B 269 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 8394) covalent geometry : angle 0.45285 / 0.24 (11475) hydrogen bonds : bond 0.05127 / 3.88 ( 389) hydrogen bonds : angle 3.90506 / 2.80 ( 1072) metal coordination : bond 0.00368 / 0.18 ( 4) metal coordination : angle 3.14895 / 1.70 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5544.69 seconds wall clock time: 94 minutes 27.87 seconds (5667.87 seconds total)