Starting phenix.real_space_refine on Thu Aug 6 17:37:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pso_17858/08_2026/8pso_17858.map" } resolution = 2.4 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= 0.004 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 31 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 5046 2.51 5 N 1459 2.21 5 O 1681 1.98 5 H 7937 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16201 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5036 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: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 406 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 8} Chain: "S" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 476 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: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CTP': 1} Classifications: {'undetermined': 1} 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': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 969 SG CYS A 161 47.014 44.089 83.490 1.00 27.60 S ATOM 2857 SG CYS A 282 45.317 46.416 86.158 1.00 26.75 S Time building chain proxies: 3.34, per 1000 atoms: 0.21 Number of scatterers: 16201 At special positions: 0 Unit cell: (88.2, 94.92, 102.48, 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 31 15.00 Mg 2 11.99 O 1681 8.00 N 1459 7.00 C 5046 6.00 H 7937 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: 1.08 Conformation dependent library (CDL) restraints added in 473.3 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: 41 helices and 10 sheets defined 48.1% alpha, 12.8% beta 7 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.657A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.540A pdb=" N GLY A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.585A pdb=" N THR A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.626A pdb=" N LEU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.511A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.930A 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 Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.579A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 removed outlier: 3.563A pdb=" N GLY B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) 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 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.737A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.809A 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 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.979A 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 496 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: 3.677A 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: 3.687A 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 Processing helix chain 'C' and resid 100 through 107 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: 6.234A 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: 6.234A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.259A 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: 3.726A pdb=" N ARG B 155 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA9, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 83 removed outlier: 7.242A pdb=" N LYS C 75 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR C 119 " --> pdb=" O LYS C 75 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.52 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: 7915 1.03 - 1.23: 32 1.23 - 1.42: 3521 1.42 - 1.61: 4838 1.61 - 1.81: 64 Bond restraints: 16370 Sorted by residual: bond pdb=" O3B CTP F 1 " pdb=" PG CTP F 1 " ideal model delta sigma weight residual 1.751 1.613 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" O3A CTP F 1 " pdb=" PB CTP F 1 " ideal model delta sigma weight residual 1.675 1.602 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" O5' CTP F 1 " pdb=" PA CTP F 1 " ideal model delta sigma weight residual 1.660 1.603 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.94e+00 bond pdb=" C5' CTP F 1 " pdb=" O5' CTP F 1 " ideal model delta sigma weight residual 1.405 1.449 -0.044 2.00e-02 2.50e+03 4.73e+00 ... (remaining 16365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 29225 1.79 - 3.58: 326 3.58 - 5.37: 16 5.37 - 7.16: 3 7.16 - 8.94: 1 Bond angle restraints: 29571 Sorted by residual: angle pdb=" CA PRO B 470 " pdb=" N PRO B 470 " pdb=" CD PRO B 470 " ideal model delta sigma weight residual 112.00 103.06 8.94 1.40e+00 5.10e-01 4.08e+01 angle pdb=" O5' A S 7 " pdb=" C5' A S 7 " pdb=" C4' A S 7 " ideal model delta sigma weight residual 109.40 112.24 -2.84 8.00e-01 1.56e+00 1.26e+01 angle pdb=" O5' G S 3 " pdb=" C5' G S 3 " pdb=" C4' G S 3 " ideal model delta sigma weight residual 109.40 112.09 -2.69 8.00e-01 1.56e+00 1.13e+01 angle pdb=" O5' C V 13 " pdb=" C5' C V 13 " pdb=" C4' C V 13 " ideal model delta sigma weight residual 109.40 111.98 -2.58 8.00e-01 1.56e+00 1.04e+01 angle pdb=" O5' A S 4 " pdb=" C5' A S 4 " pdb=" C4' A S 4 " ideal model delta sigma weight residual 109.40 111.90 -2.50 8.00e-01 1.56e+00 9.74e+00 ... (remaining 29566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 7393 34.72 - 69.44: 321 69.44 - 104.16: 27 104.16 - 138.88: 0 138.88 - 173.61: 1 Dihedral angle restraints: 7742 sinusoidal: 4499 harmonic: 3243 Sorted by residual: dihedral pdb=" C4' G S 1 " pdb=" C3' G S 1 " pdb=" O3' G S 1 " pdb=" P U S 2 " ideal model delta sinusoidal sigma weight residual -110.00 63.61 -173.61 1 3.50e+01 8.16e-04 1.56e+01 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 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB GLU A 287 " pdb=" CG GLU A 287 " pdb=" CD GLU A 287 " pdb=" OE1 GLU A 287 " ideal model delta sinusoidal sigma weight residual 0.00 -89.78 89.78 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1058 0.041 - 0.081: 173 0.081 - 0.122: 87 0.122 - 0.163: 8 0.163 - 0.203: 1 Chirality restraints: 1327 Sorted by residual: chirality pdb=" C2' CTP F 1 " pdb=" C1' CTP F 1 " pdb=" C3' CTP F 1 " pdb=" O2' CTP F 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.72 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1' CTP F 1 " pdb=" C2' CTP F 1 " pdb=" N1 CTP F 1 " pdb=" O4' CTP F 1 " both_signs ideal model delta sigma weight residual False 2.35 2.50 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" C3' G S 1 " pdb=" C4' G S 1 " pdb=" O3' G S 1 " pdb=" C2' G S 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1324 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 469 " -0.057 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO B 470 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 161 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO B 162 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A S 8 " -0.022 2.00e-02 2.50e+03 9.61e-03 3.00e+00 pdb=" N9 A S 8 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A S 8 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A S 8 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A S 8 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A S 8 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A S 8 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A S 8 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" H8 A S 8 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A S 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 537 2.15 - 2.76: 29691 2.76 - 3.37: 46745 3.37 - 3.99: 62048 3.99 - 4.60: 95312 Nonbonded interactions: 234333 Sorted by model distance: nonbonded pdb=" OE1 GLU C 89 " pdb=" H GLU C 89 " model vdw 1.532 2.450 nonbonded pdb=" OD2 ASP B 222 " pdb="HH22 ARG B 247 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASP B 444 " pdb=" H ASP B 444 " model vdw 1.628 2.450 nonbonded pdb=" HZ3 LYS B 249 " pdb=" O CYS B 260 " model vdw 1.637 2.450 nonbonded pdb=" HH TYR B 186 " pdb=" O SER B 286 " model vdw 1.639 2.450 ... (remaining 234328 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: 2.640 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: 0.060 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 21.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 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 0.138 8437 Z= 0.147 Angle : 0.532 8.944 11535 Z= 0.314 Chirality : 0.038 0.203 1327 Planarity : 0.005 0.082 1376 Dihedral : 18.700 173.606 3368 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 19.90 % Favored : 78.55 % 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: 1.47 (0.27), residues: 965 helix: 2.12 (0.25), residues: 421 sheet: 0.72 (0.52), residues: 93 loop : -0.03 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 206 TYR 0.008 0.001 TYR A 403 PHE 0.009 0.001 PHE C 44 TRP 0.004 0.001 TRP A 346 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8433) covalent geometry : angle 0.53154 / 0.31 (11533) hydrogen bonds : bond 0.12060 / 8.81 ( 389) hydrogen bonds : angle 4.95017 / 3.60 ( 1060) metal coordination : bond 0.00502 / 0.36 ( 4) metal coordination : angle 0.60854 / 0.21 ( 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 129 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 126 average time/residue: 1.2421 time to fit residues: 165.0350 Evaluate side-chains 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 87 THR 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: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.093851 restraints weight = 22511.023| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.27 r_work: 0.2842 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8437 Z= 0.178 Angle : 0.543 5.403 11535 Z= 0.290 Chirality : 0.039 0.233 1327 Planarity : 0.005 0.045 1376 Dihedral : 14.406 168.422 1529 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 18.12 % Favored : 79.98 % 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: 1.37 (0.27), residues: 965 helix: 1.98 (0.25), residues: 428 sheet: 0.65 (0.52), residues: 93 loop : -0.05 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 206 TYR 0.013 0.001 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.006 0.001 TRP B 432 HIS 0.006 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8433) covalent geometry : angle 0.54279 / 0.29 (11533) hydrogen bonds : bond 0.05680 / 4.05 ( 389) hydrogen bonds : angle 4.37139 / 3.16 ( 1060) metal coordination : bond 0.00856 / 0.54 ( 4) metal coordination : angle 0.10254 / 0.05 ( 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 132 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8283 (ttp80) outliers start: 16 outliers final: 11 residues processed: 128 average time/residue: 1.2573 time to fit residues: 169.9942 Evaluate side-chains 124 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094736 restraints weight = 22891.166| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.28 r_work: 0.2857 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8437 Z= 0.119 Angle : 0.502 4.960 11535 Z= 0.267 Chirality : 0.037 0.232 1327 Planarity : 0.004 0.048 1376 Dihedral : 13.951 166.852 1525 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.31 % Allowed : 18.36 % Favored : 80.33 % 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: 1.98 (0.25), residues: 428 sheet: 0.67 (0.52), residues: 93 loop : -0.09 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 475 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.005 0.001 TRP B 432 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8433) covalent geometry : angle 0.50178 / 0.27 (11533) hydrogen bonds : bond 0.04902 / 3.49 ( 389) hydrogen bonds : angle 4.24360 / 3.07 ( 1060) metal coordination : bond 0.00735 / 0.49 ( 4) metal coordination : angle 0.23896 / 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 127 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.410 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 1.3780 time to fit residues: 181.8074 Evaluate side-chains 118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 66 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.094097 restraints weight = 22669.885| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.28 r_work: 0.2840 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8437 Z= 0.139 Angle : 0.511 4.781 11535 Z= 0.273 Chirality : 0.038 0.226 1327 Planarity : 0.004 0.053 1376 Dihedral : 13.838 166.282 1523 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.55 % Allowed : 18.12 % Favored : 80.33 % 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: 1.27 (0.27), residues: 965 helix: 1.92 (0.25), residues: 428 sheet: 0.69 (0.52), residues: 93 loop : -0.14 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 475 TYR 0.013 0.001 TYR A 403 PHE 0.015 0.001 PHE C 44 TRP 0.006 0.001 TRP B 432 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8433) covalent geometry : angle 0.51057 / 0.27 (11533) hydrogen bonds : bond 0.04995 / 3.56 ( 389) hydrogen bonds : angle 4.20258 / 3.03 ( 1060) metal coordination : bond 0.00845 / 0.55 ( 4) metal coordination : angle 0.18949 / 0.07 ( 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 126 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7962 (mmp-170) outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 1.4419 time to fit residues: 185.7437 Evaluate side-chains 117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093605 restraints weight = 22678.685| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.27 r_work: 0.2827 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8437 Z= 0.151 Angle : 0.524 4.714 11535 Z= 0.280 Chirality : 0.038 0.221 1327 Planarity : 0.004 0.055 1376 Dihedral : 13.805 165.660 1523 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.31 % Allowed : 18.12 % Favored : 80.57 % 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: 1.19 (0.27), residues: 965 helix: 1.84 (0.25), residues: 428 sheet: 0.55 (0.51), residues: 95 loop : -0.15 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 475 TYR 0.013 0.001 TYR A 403 PHE 0.016 0.002 PHE C 44 TRP 0.006 0.001 TRP B 432 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8433) covalent geometry : angle 0.52369 / 0.28 (11533) hydrogen bonds : bond 0.05144 / 3.67 ( 389) hydrogen bonds : angle 4.21236 / 3.04 ( 1060) metal coordination : bond 0.00857 / 0.55 ( 4) metal coordination : angle 0.22634 / 0.10 ( 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 122 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (mmp-170) REVERT: A 332 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8317 (ttp80) outliers start: 11 outliers final: 6 residues processed: 119 average time/residue: 1.4776 time to fit residues: 185.3103 Evaluate side-chains 118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.092646 restraints weight = 22645.574| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.30 r_work: 0.2822 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8437 Z= 0.157 Angle : 0.531 4.738 11535 Z= 0.284 Chirality : 0.039 0.218 1327 Planarity : 0.004 0.057 1376 Dihedral : 13.760 165.228 1522 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.43 % Allowed : 17.88 % Favored : 80.69 % 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: 1.13 (0.26), residues: 965 helix: 1.77 (0.25), residues: 428 sheet: 0.56 (0.50), residues: 95 loop : -0.17 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 475 TYR 0.013 0.001 TYR A 403 PHE 0.016 0.002 PHE C 82 TRP 0.007 0.001 TRP A 346 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8433) covalent geometry : angle 0.53080 / 0.28 (11533) hydrogen bonds : bond 0.05254 / 3.73 ( 389) hydrogen bonds : angle 4.22649 / 3.05 ( 1060) metal coordination : bond 0.01002 / 0.64 ( 4) metal coordination : angle 0.20321 / 0.09 ( 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 123 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 189 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7926 (mmp-170) REVERT: A 332 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8336 (ttp80) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 1.5246 time to fit residues: 190.8990 Evaluate side-chains 117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094449 restraints weight = 22869.616| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.27 r_work: 0.2860 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 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: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8437 Z= 0.108 Angle : 0.498 4.813 11535 Z= 0.265 Chirality : 0.037 0.221 1327 Planarity : 0.004 0.072 1376 Dihedral : 13.415 164.624 1522 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.19 % Allowed : 17.76 % Favored : 81.05 % 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: 1.27 (0.27), residues: 965 helix: 1.91 (0.25), residues: 429 sheet: 0.58 (0.51), residues: 95 loop : -0.12 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 475 TYR 0.011 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.006 0.001 TRP B 432 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8433) covalent geometry : angle 0.49781 / 0.27 (11533) hydrogen bonds : bond 0.04547 / 3.24 ( 389) hydrogen bonds : angle 4.13975 / 2.99 ( 1060) metal coordination : bond 0.00675 / 0.46 ( 4) metal coordination : angle 0.33568 / 0.12 ( 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 120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8290 (ttp80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 1.4860 time to fit residues: 183.1578 Evaluate side-chains 115 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094382 restraints weight = 22589.672| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.27 r_work: 0.2856 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8437 Z= 0.121 Angle : 0.499 4.783 11535 Z= 0.266 Chirality : 0.037 0.218 1327 Planarity : 0.004 0.065 1376 Dihedral : 13.316 164.732 1521 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.31 % Allowed : 17.88 % Favored : 80.81 % 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: 965 helix: 1.91 (0.25), residues: 429 sheet: 0.59 (0.51), residues: 95 loop : -0.13 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 475 TYR 0.012 0.001 TYR A 403 PHE 0.013 0.001 PHE C 44 TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8433) covalent geometry : angle 0.49922 / 0.27 (11533) hydrogen bonds : bond 0.04656 / 3.32 ( 389) hydrogen bonds : angle 4.11240 / 2.97 ( 1060) metal coordination : bond 0.00779 / 0.51 ( 4) metal coordination : angle 0.26842 / 0.10 ( 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 120 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8304 (ttp80) REVERT: B 486 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.7053 (mt) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 1.5193 time to fit residues: 188.4707 Evaluate side-chains 117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093185 restraints weight = 22759.821| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.27 r_work: 0.2832 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8437 Z= 0.164 Angle : 0.530 4.848 11535 Z= 0.283 Chirality : 0.039 0.214 1327 Planarity : 0.004 0.059 1376 Dihedral : 13.459 164.963 1521 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.31 % Allowed : 17.88 % Favored : 80.81 % 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: 1.15 (0.27), residues: 965 helix: 1.82 (0.25), residues: 429 sheet: 0.54 (0.51), residues: 95 loop : -0.19 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 475 TYR 0.013 0.001 TYR A 403 PHE 0.016 0.002 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 0.00371 / 0.16 ( 8433) covalent geometry : angle 0.52960 / 0.28 (11533) hydrogen bonds : bond 0.05101 / 3.63 ( 389) hydrogen bonds : angle 4.16040 / 3.00 ( 1060) metal coordination : bond 0.00875 / 0.55 ( 4) metal coordination : angle 0.25229 / 0.12 ( 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 119 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8333 (ttp80) REVERT: B 486 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.7050 (mt) outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 1.4866 time to fit residues: 181.9307 Evaluate side-chains 115 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.119211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.093504 restraints weight = 22871.253| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.28 r_work: 0.2843 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8437 Z= 0.127 Angle : 0.509 4.819 11535 Z= 0.270 Chirality : 0.038 0.218 1327 Planarity : 0.004 0.057 1376 Dihedral : 13.391 164.543 1521 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.07 % Allowed : 18.36 % Favored : 80.57 % 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: 965 helix: 1.86 (0.25), residues: 429 sheet: 0.56 (0.51), residues: 95 loop : -0.16 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 475 TYR 0.012 0.001 TYR A 403 PHE 0.014 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 0.00284 / 0.13 ( 8433) covalent geometry : angle 0.50860 / 0.27 (11533) hydrogen bonds : bond 0.04792 / 3.41 ( 389) hydrogen bonds : angle 4.13515 / 2.98 ( 1060) metal coordination : bond 0.00810 / 0.53 ( 4) metal coordination : angle 0.26659 / 0.11 ( 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 117 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: B 486 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.7010 (mt) outliers start: 9 outliers final: 4 residues processed: 115 average time/residue: 1.4293 time to fit residues: 173.1200 Evaluate side-chains 118 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 GLN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094637 restraints weight = 22620.363| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.27 r_work: 0.2855 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8437 Z= 0.111 Angle : 0.494 4.757 11535 Z= 0.262 Chirality : 0.037 0.218 1327 Planarity : 0.004 0.055 1376 Dihedral : 13.247 164.349 1521 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.07 % Allowed : 18.24 % Favored : 80.69 % 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: 1.27 (0.27), residues: 965 helix: 1.92 (0.25), residues: 429 sheet: 0.68 (0.52), residues: 93 loop : -0.15 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 475 TYR 0.012 0.001 TYR A 403 PHE 0.012 0.001 PHE C 44 TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8433) covalent geometry : angle 0.49401 / 0.26 (11533) hydrogen bonds : bond 0.04542 / 3.23 ( 389) hydrogen bonds : angle 4.09099 / 2.95 ( 1060) metal coordination : bond 0.00724 / 0.48 ( 4) metal coordination : angle 0.37412 / 0.14 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6425.90 seconds wall clock time: 109 minutes 26.22 seconds (6566.22 seconds total)