Starting phenix.real_space_refine on Fri Jul 3 21:25:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psu_17862/07_2026/8psu_17862.cif" } resolution = 3.18 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 29 5.49 5 S 44 5.16 5 C 5047 2.51 5 N 1461 2.21 5 O 1630 1.98 5 H 7957 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 16169 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5035 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 18, 'TRANS': 297} Chain: "B" Number of atoms: 7974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} Conformer: "B" Number of residues, atoms: 515, 7973 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 493} bond proxies already assigned to first conformer: 8044 Chain: "C" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2233 Classifications: {'peptide': 140} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "V" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 440 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 3, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 8} Chain: "S" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 486 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 968 SG CYS A 161 53.348 48.182 17.600 1.00 42.34 S ATOM 2856 SG CYS A 282 52.801 45.100 15.249 1.00 54.27 S Time building chain proxies: 4.07, per 1000 atoms: 0.25 Number of scatterers: 16169 At special positions: 0 Unit cell: (86.9, 97.9, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 44 16.00 P 29 15.00 O 1630 8.00 N 1461 7.00 C 5047 6.00 H 7957 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: 1.46 Conformation dependent library (CDL) restraints added in 619.4 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 161 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " Number of angles added : 2 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 47.3% alpha, 12.8% beta 7 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.679A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.703A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.662A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.544A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.558A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.947A 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 388 through 392 removed outlier: 3.731A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.911A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 66 through 70 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 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 236 through 248 removed outlier: 3.714A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.035A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.906A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.972A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.504A pdb=" N LYS B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.558A pdb=" N HIS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.552A 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 98 removed outlier: 3.522A pdb=" N GLY C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.589A pdb=" N THR B 293 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.102A 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: 6.102A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.378A 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: 3.798A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 326 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 72 through 83 removed outlier: 7.099A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 3.88 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: 7935 1.03 - 1.23: 33 1.23 - 1.42: 3529 1.42 - 1.61: 4825 1.61 - 1.81: 64 Bond restraints: 16386 Sorted by residual: bond pdb=" C LEU B 144 " pdb=" N ARG B 145 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.46e-02 4.69e+03 1.15e+01 bond pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 1.327 1.302 0.025 1.47e-02 4.63e+03 2.94e+00 bond pdb=" C VAL B 170 " pdb=" O VAL B 170 " ideal model delta sigma weight residual 1.237 1.246 -0.010 1.13e-02 7.83e+03 7.17e-01 bond pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.23e-01 bond pdb=" C LEU B 166 " pdb=" O LEU B 166 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.22e-01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 27081 0.91 - 1.81: 2298 1.81 - 2.72: 165 2.72 - 3.63: 59 3.63 - 4.53: 9 Bond angle restraints: 29612 Sorted by residual: angle pdb=" N ASP A 380 " pdb=" CA ASP A 380 " pdb=" CB ASP A 380 " ideal model delta sigma weight residual 113.65 110.09 3.56 1.47e+00 4.63e-01 5.87e+00 angle pdb=" C PHE B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 121.54 125.83 -4.29 1.91e+00 2.74e-01 5.04e+00 angle pdb=" O ARG B 145 " pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 123.22 121.06 2.16 1.14e+00 7.69e-01 3.58e+00 angle pdb=" CA ARG B 145 " pdb=" C ARG B 145 " pdb=" N ASP B 146 " ideal model delta sigma weight residual 116.37 118.68 -2.31 1.23e+00 6.61e-01 3.51e+00 angle pdb=" CB ARG A 189 " pdb=" CG ARG A 189 " pdb=" CD ARG A 189 " ideal model delta sigma weight residual 111.30 115.20 -3.90 2.30e+00 1.89e-01 2.87e+00 ... (remaining 29607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6764 17.94 - 35.88: 625 35.88 - 53.82: 222 53.82 - 71.77: 50 71.77 - 89.71: 14 Dihedral angle restraints: 7675 sinusoidal: 4433 harmonic: 3242 Sorted by residual: dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual 180.00 -162.98 -17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" O4' U V 10 " pdb=" C1' U V 10 " pdb=" N1 U V 10 " pdb=" C2 U V 10 " ideal model delta sinusoidal sigma weight residual -128.00 -176.52 48.52 1 1.70e+01 3.46e-03 1.12e+01 dihedral pdb=" CB GLU A 326 " pdb=" CG GLU A 326 " pdb=" CD GLU A 326 " pdb=" OE1 GLU A 326 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 871 0.028 - 0.056: 342 0.056 - 0.084: 57 0.084 - 0.112: 44 0.112 - 0.140: 14 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE B 253 " pdb=" N ILE B 253 " pdb=" C ILE B 253 " pdb=" CB ILE B 253 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL B 417 " pdb=" N VAL B 417 " pdb=" C VAL B 417 " pdb=" CB VAL B 417 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-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 4.37e-01 ... (remaining 1325 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 162 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.021 2.00e-02 2.50e+03 8.36e-03 2.27e+00 pdb=" N9 A V 4 " -0.019 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" H8 A V 4 " -0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 470 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.019 5.00e-02 4.00e+02 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 31731 2.79 - 3.40: 43845 3.40 - 4.00: 58522 4.00 - 4.60: 91055 Nonbonded interactions: 226098 Sorted by model distance: nonbonded pdb=" HH TYR B 186 " pdb=" O SER B 286 " model vdw 1.589 2.450 nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.605 2.450 nonbonded pdb=" O PHE B 164 " pdb=" HG SER B 168 " model vdw 1.630 2.450 nonbonded pdb=" O GLY A 309 " pdb="HH22 ARG B 394 " model vdw 1.651 2.450 nonbonded pdb=" HG SER C 121 " pdb=" OD1 ASP C 125 " model vdw 1.658 2.450 ... (remaining 226093 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=0.40 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 23.660 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 0.049 8433 Z= 0.114 Angle : 0.446 4.533 11529 Z= 0.235 Chirality : 0.035 0.140 1328 Planarity : 0.003 0.048 1376 Dihedral : 17.012 89.707 3308 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 16.45 % Favored : 83.55 % 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: 1.54 (0.28), residues: 965 helix: 2.19 (0.26), residues: 432 sheet: -0.05 (0.51), residues: 103 loop : 0.16 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 461 TYR 0.010 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.003 0.001 TRP A 346 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8429) covalent geometry : angle 0.44642 / 0.23 (11527) hydrogen bonds : bond 0.13189 / 8.56 ( 377) hydrogen bonds : angle 4.92140 / 3.57 ( 1045) metal coordination : bond 0.00597 / 0.39 ( 4) metal coordination : angle 0.10238 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2718 time to fit residues: 31.3371 Evaluate side-chains 89 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.088045 restraints weight = 30347.064| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.76 r_work: 0.2779 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8433 Z= 0.163 Angle : 0.490 4.633 11529 Z= 0.257 Chirality : 0.037 0.159 1328 Planarity : 0.004 0.051 1376 Dihedral : 11.140 74.002 1458 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 0.60 % Allowed : 15.85 % Favored : 83.55 % 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 (0.28), residues: 965 helix: 2.13 (0.26), residues: 434 sheet: 0.01 (0.52), residues: 103 loop : 0.06 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.014 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 8429) covalent geometry : angle 0.48985 / 0.26 (11527) hydrogen bonds : bond 0.04714 / 3.45 ( 377) hydrogen bonds : angle 4.12613 / 3.01 ( 1045) metal coordination : bond 0.00956 / 0.53 ( 4) metal coordination : angle 0.51061 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.450 Fit side-chains REVERT: B 218 ASN cc_start: 0.8467 (m-40) cc_final: 0.8256 (m-40) outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 0.2757 time to fit residues: 34.3780 Evaluate side-chains 95 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 389 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.115410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090296 restraints weight = 30461.450| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.76 r_work: 0.2795 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8433 Z= 0.106 Angle : 0.445 4.495 11529 Z= 0.233 Chirality : 0.035 0.153 1328 Planarity : 0.003 0.049 1376 Dihedral : 11.041 74.316 1458 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.07 % Favored : 97.72 % Rotamer: Outliers : 0.60 % Allowed : 15.61 % Favored : 83.79 % 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: 1.52 (0.28), residues: 965 helix: 2.22 (0.26), residues: 435 sheet: 0.12 (0.52), residues: 103 loop : 0.03 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 8429) covalent geometry : angle 0.44481 / 0.23 (11527) hydrogen bonds : bond 0.03912 / 2.90 ( 377) hydrogen bonds : angle 3.89295 / 2.86 ( 1045) metal coordination : bond 0.00502 / 0.33 ( 4) metal coordination : angle 0.26004 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 218 ASN cc_start: 0.8421 (m-40) cc_final: 0.8187 (m-40) REVERT: B 461 ARG cc_start: 0.7793 (tpp80) cc_final: 0.6989 (mpp80) REVERT: C 3 GLN cc_start: 0.5764 (mm-40) cc_final: 0.5551 (mm110) REVERT: C 55 ASP cc_start: 0.7681 (t0) cc_final: 0.6930 (m-30) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 0.2958 time to fit residues: 36.3547 Evaluate side-chains 96 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 88 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.088532 restraints weight = 30395.123| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.78 r_work: 0.2784 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8433 Z= 0.140 Angle : 0.465 4.561 11529 Z= 0.245 Chirality : 0.036 0.155 1328 Planarity : 0.004 0.051 1376 Dihedral : 11.083 74.430 1458 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.07 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 15.49 % Favored : 83.67 % 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: 1.39 (0.27), residues: 965 helix: 2.12 (0.25), residues: 435 sheet: 0.09 (0.53), residues: 103 loop : -0.07 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 353 TYR 0.013 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8429) covalent geometry : angle 0.46525 / 0.24 (11527) hydrogen bonds : bond 0.04237 / 3.15 ( 377) hydrogen bonds : angle 3.92575 / 2.88 ( 1045) metal coordination : bond 0.00746 / 0.42 ( 4) metal coordination : angle 0.30855 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.306 Fit side-chains REVERT: B 218 ASN cc_start: 0.8405 (m-40) cc_final: 0.8108 (m-40) REVERT: C 138 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8271 (mt) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.2877 time to fit residues: 34.5281 Evaluate side-chains 94 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.087894 restraints weight = 30450.290| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.80 r_work: 0.2745 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8433 Z= 0.144 Angle : 0.467 4.567 11529 Z= 0.246 Chirality : 0.036 0.156 1328 Planarity : 0.004 0.051 1376 Dihedral : 11.091 74.435 1458 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.28 % Favored : 97.51 % Rotamer: Outliers : 0.95 % Allowed : 15.49 % Favored : 83.55 % 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: 1.34 (0.27), residues: 965 helix: 2.09 (0.25), residues: 435 sheet: 0.05 (0.52), residues: 103 loop : -0.11 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.013 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 8429) covalent geometry : angle 0.46651 / 0.25 (11527) hydrogen bonds : bond 0.04214 / 3.13 ( 377) hydrogen bonds : angle 3.93183 / 2.89 ( 1045) metal coordination : bond 0.00741 / 0.44 ( 4) metal coordination : angle 0.51304 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.385 Fit side-chains REVERT: A 105 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7782 (mttp) REVERT: A 263 LYS cc_start: 0.7040 (tttt) cc_final: 0.6778 (ttpt) REVERT: C 138 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8264 (mt) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.2859 time to fit residues: 33.2020 Evaluate side-chains 97 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.090203 restraints weight = 30231.390| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.80 r_work: 0.2807 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8433 Z= 0.088 Angle : 0.428 4.442 11529 Z= 0.224 Chirality : 0.035 0.149 1328 Planarity : 0.003 0.048 1376 Dihedral : 10.962 74.184 1458 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.93 % Rotamer: Outliers : 0.95 % Allowed : 15.61 % Favored : 83.43 % 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: 1.61 (0.28), residues: 965 helix: 2.34 (0.26), residues: 436 sheet: 0.22 (0.53), residues: 103 loop : -0.01 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 111 TYR 0.010 0.001 TYR A 403 PHE 0.007 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.002 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 8429) covalent geometry : angle 0.42829 / 0.22 (11527) hydrogen bonds : bond 0.03432 / 2.57 ( 377) hydrogen bonds : angle 3.73272 / 2.75 ( 1045) metal coordination : bond 0.00477 / 0.32 ( 4) metal coordination : angle 0.30715 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7694 (mttp) REVERT: B 218 ASN cc_start: 0.8391 (m-40) cc_final: 0.8176 (m-40) REVERT: C 138 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (mt) outliers start: 8 outliers final: 7 residues processed: 103 average time/residue: 0.2756 time to fit residues: 35.8359 Evaluate side-chains 99 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.089736 restraints weight = 30115.919| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.76 r_work: 0.2800 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8433 Z= 0.117 Angle : 0.445 4.524 11529 Z= 0.233 Chirality : 0.035 0.154 1328 Planarity : 0.004 0.049 1376 Dihedral : 10.972 74.350 1458 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.95 % Allowed : 15.73 % Favored : 83.31 % 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: 1.53 (0.28), residues: 965 helix: 2.28 (0.26), residues: 436 sheet: 0.14 (0.52), residues: 103 loop : -0.05 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8429) covalent geometry : angle 0.44477 / 0.23 (11527) hydrogen bonds : bond 0.03809 / 2.84 ( 377) hydrogen bonds : angle 3.78969 / 2.79 ( 1045) metal coordination : bond 0.00580 / 0.35 ( 4) metal coordination : angle 0.32733 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7748 (mttp) REVERT: A 263 LYS cc_start: 0.6935 (tttt) cc_final: 0.6703 (ttpt) REVERT: C 138 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8254 (mt) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.2802 time to fit residues: 34.3434 Evaluate side-chains 96 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.088792 restraints weight = 30432.502| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.75 r_work: 0.2771 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8433 Z= 0.160 Angle : 0.480 4.649 11529 Z= 0.253 Chirality : 0.037 0.158 1328 Planarity : 0.004 0.051 1376 Dihedral : 11.113 74.510 1458 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 0.95 % Allowed : 16.21 % Favored : 82.84 % 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: 1.31 (0.27), residues: 965 helix: 2.10 (0.25), residues: 435 sheet: -0.02 (0.51), residues: 103 loop : -0.14 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.014 0.001 TYR A 403 PHE 0.010 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.005 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 8429) covalent geometry : angle 0.47990 / 0.25 (11527) hydrogen bonds : bond 0.04394 / 3.26 ( 377) hydrogen bonds : angle 3.93929 / 2.88 ( 1045) metal coordination : bond 0.00850 / 0.49 ( 4) metal coordination : angle 0.53055 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.445 Fit side-chains REVERT: A 105 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7800 (mttp) REVERT: B 461 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7537 (ttm110) REVERT: C 88 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: C 138 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8241 (mt) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.2691 time to fit residues: 33.7974 Evaluate side-chains 97 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.121214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.097445 restraints weight = 29638.865| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.63 r_work: 0.2837 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8433 Z= 0.096 Angle : 0.438 4.461 11529 Z= 0.231 Chirality : 0.035 0.150 1328 Planarity : 0.003 0.049 1376 Dihedral : 10.993 74.235 1458 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.07 % Favored : 97.82 % Rotamer: Outliers : 0.95 % Allowed : 16.33 % Favored : 82.72 % 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: 1.52 (0.28), residues: 965 helix: 2.31 (0.26), residues: 435 sheet: 0.10 (0.52), residues: 103 loop : -0.07 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.011 0.001 TYR A 403 PHE 0.008 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.002 0.000 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8429) covalent geometry : angle 0.43799 / 0.23 (11527) hydrogen bonds : bond 0.03640 / 2.72 ( 377) hydrogen bonds : angle 3.79272 / 2.79 ( 1045) metal coordination : bond 0.00443 / 0.29 ( 4) metal coordination : angle 0.36987 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7718 (mttp) REVERT: A 323 ASP cc_start: 0.8134 (t70) cc_final: 0.7780 (t70) REVERT: B 461 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7480 (ttm110) REVERT: C 88 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: C 138 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8207 (mt) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.2685 time to fit residues: 34.6142 Evaluate side-chains 104 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096058 restraints weight = 29799.617| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.66 r_work: 0.2853 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8433 Z= 0.120 Angle : 0.454 4.511 11529 Z= 0.238 Chirality : 0.035 0.154 1328 Planarity : 0.004 0.049 1376 Dihedral : 11.004 74.303 1458 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.51 % Rotamer: Outliers : 0.95 % Allowed : 16.57 % Favored : 82.48 % 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: 1.49 (0.28), residues: 965 helix: 2.28 (0.26), residues: 435 sheet: 0.06 (0.52), residues: 103 loop : -0.09 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.012 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8429) covalent geometry : angle 0.45408 / 0.24 (11527) hydrogen bonds : bond 0.03842 / 2.86 ( 377) hydrogen bonds : angle 3.81025 / 2.80 ( 1045) metal coordination : bond 0.00600 / 0.36 ( 4) metal coordination : angle 0.35989 / 0.15 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7735 (mttp) REVERT: B 461 ARG cc_start: 0.7742 (tpp80) cc_final: 0.7511 (ttm110) REVERT: C 55 ASP cc_start: 0.7551 (t0) cc_final: 0.6829 (m-30) REVERT: C 138 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8239 (mt) outliers start: 8 outliers final: 7 residues processed: 101 average time/residue: 0.2448 time to fit residues: 31.7644 Evaluate side-chains 102 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.089818 restraints weight = 30350.531| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.76 r_work: 0.2798 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8433 Z= 0.103 Angle : 0.440 4.476 11529 Z= 0.231 Chirality : 0.035 0.150 1328 Planarity : 0.003 0.049 1376 Dihedral : 10.950 74.218 1458 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.07 % Favored : 97.82 % Rotamer: Outliers : 0.95 % Allowed : 16.57 % Favored : 82.48 % 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: 1.58 (0.28), residues: 965 helix: 2.36 (0.26), residues: 435 sheet: 0.12 (0.52), residues: 103 loop : -0.06 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.011 0.001 TYR A 403 PHE 0.008 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 8429) covalent geometry : angle 0.44021 / 0.23 (11527) hydrogen bonds : bond 0.03613 / 2.70 ( 377) hydrogen bonds : angle 3.75311 / 2.76 ( 1045) metal coordination : bond 0.00467 / 0.29 ( 4) metal coordination : angle 0.37129 / 0.14 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.56 seconds wall clock time: 64 minutes 32.88 seconds (3872.88 seconds total)