Starting phenix.real_space_refine on Fri Oct 23 05:55:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb0_21583/10_2026/6wb0_21583.map" } resolution = 4.2 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 6 5.16 5 C 5186 2.51 5 N 1481 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 3911 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 510} Chain breaks: 3 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLU:plan': 32, 'ASP:plan': 12, 'TRP:plan': 1, 'GLN:plan1': 9, 'TYR:plan': 3, 'ARG:plan': 6, 'PHE:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2979 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 30, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 10, 'GLN:plan1': 5, 'TRP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 168 Chain: "C" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 747 Classifications: {'RNAv2': 35} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna3p': 34} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 881 Classifications: {'DNA': 4, 'RNAv2': 38} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8518 At special positions: 0 Unit cell: (104.94, 107.06, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 74 15.00 O 1771 8.00 N 1481 7.00 C 5186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 218.4 milliseconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.6% alpha, 6.3% beta 39 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.292A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.779A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.256A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.579A pdb=" N HIS A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.514A pdb=" N TRP A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.678A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.217A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 4.059A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.005A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 4.139A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.165A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.504A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.140A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.815A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 5.158A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.883A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 4.461A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.944A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.724A pdb=" N LYS B 281 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 283 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.870A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.853A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.519A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.866A pdb=" N GLY A 190 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 179 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.304A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA5, first strand: chain 'A' and resid 439 through 441 removed outlier: 6.524A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.569A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62 removed outlier: 4.539A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.050A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.479A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 293 " --> pdb=" O TRP B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.858A pdb=" N THR B 338 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 330 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2420 1.34 - 1.45: 1856 1.45 - 1.57: 4461 1.57 - 1.69: 147 1.69 - 1.81: 9 Bond restraints: 8893 Sorted by residual: bond pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" C5 DC D 77 " pdb=" C6 DC D 77 " ideal model delta sigma weight residual 1.339 1.361 -0.022 8.00e-03 1.56e+04 7.38e+00 bond pdb=" N1 DC D 77 " pdb=" C6 DC D 77 " ideal model delta sigma weight residual 1.367 1.357 0.010 6.00e-03 2.78e+04 2.53e+00 bond pdb=" N1 DT D 78 " pdb=" C2 DT D 78 " ideal model delta sigma weight residual 1.376 1.388 -0.012 8.00e-03 1.56e+04 2.37e+00 bond pdb=" C2 DT D 78 " pdb=" O2 DT D 78 " ideal model delta sigma weight residual 1.220 1.232 -0.012 8.00e-03 1.56e+04 2.12e+00 ... (remaining 8888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11978 1.31 - 2.62: 352 2.62 - 3.93: 199 3.93 - 5.24: 8 5.24 - 6.55: 3 Bond angle restraints: 12540 Sorted by residual: angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 112.00 106.61 5.39 1.40e+00 5.10e-01 1.48e+01 angle pdb=" O4' DC D 77 " pdb=" C4' DC D 77 " pdb=" C3' DC D 77 " ideal model delta sigma weight residual 106.00 103.88 2.12 6.00e-01 2.78e+00 1.24e+01 angle pdb=" O4' DT D 78 " pdb=" C4' DT D 78 " pdb=" C3' DT D 78 " ideal model delta sigma weight residual 106.00 103.98 2.02 6.00e-01 2.78e+00 1.13e+01 angle pdb=" O4' DG D 79 " pdb=" C4' DG D 79 " pdb=" C3' DG D 79 " ideal model delta sigma weight residual 106.00 104.02 1.98 6.00e-01 2.78e+00 1.09e+01 angle pdb=" O4' DG D 73 " pdb=" C4' DG D 73 " pdb=" C3' DG D 73 " ideal model delta sigma weight residual 106.00 104.08 1.92 6.00e-01 2.78e+00 1.02e+01 ... (remaining 12535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4661 17.60 - 35.21: 242 35.21 - 52.81: 120 52.81 - 70.42: 23 70.42 - 88.02: 5 Dihedral angle restraints: 5051 sinusoidal: 2290 harmonic: 2761 Sorted by residual: dihedral pdb=" O5' A D 50 " pdb=" C5' A D 50 " pdb=" C4' A D 50 " pdb=" C3' A D 50 " ideal model delta sinusoidal sigma weight residual -60.00 -7.52 -52.48 3 6.40e+00 2.44e-02 5.01e+01 dihedral pdb=" O5' C C 175 " pdb=" C5' C C 175 " pdb=" C4' C C 175 " pdb=" C3' C C 175 " ideal model delta sinusoidal sigma weight residual 60.00 103.48 -43.48 3 6.40e+00 2.44e-02 4.29e+01 dihedral pdb=" O5' U D 47 " pdb=" C5' U D 47 " pdb=" C4' U D 47 " pdb=" C3' U D 47 " ideal model delta sinusoidal sigma weight residual 60.00 103.08 -43.08 3 6.40e+00 2.44e-02 4.25e+01 ... (remaining 5048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1161 0.051 - 0.102: 202 0.102 - 0.153: 57 0.153 - 0.205: 0 0.205 - 0.256: 74 Chirality restraints: 1494 Sorted by residual: chirality pdb=" P G D 53 " pdb=" OP1 G D 53 " pdb=" OP2 G D 53 " pdb=" O5' G D 53 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' DT D 78 " pdb=" C4' DT D 78 " pdb=" O3' DT D 78 " pdb=" C2' DT D 78 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" P G D 52 " pdb=" OP1 G D 52 " pdb=" OP2 G D 52 " pdb=" O5' G D 52 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1491 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 58 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 59 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 168 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.84e+00 pdb=" C LEU A 168 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU A 168 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 169 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 78 " 0.010 2.00e-02 2.50e+03 7.49e-03 1.40e+00 pdb=" N1 DT D 78 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DT D 78 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT D 78 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DT D 78 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT D 78 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT D 78 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT D 78 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT D 78 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT D 78 " -0.008 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 320 2.68 - 3.24: 8326 3.24 - 3.79: 13760 3.79 - 4.35: 17343 4.35 - 4.90: 26029 Nonbonded interactions: 65778 Sorted by model distance: nonbonded pdb=" C TYR A 339 " pdb=" OE1 GLN A 340 " model vdw 2.131 3.270 nonbonded pdb=" OP2 A C 203 " pdb=" N6 A D 50 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS A 350 " pdb=" OE2 GLU A 378 " model vdw 2.221 3.120 nonbonded pdb=" N PHE B 61 " pdb=" CD1 PHE B 61 " model vdw 2.232 3.420 nonbonded pdb=" O2' A D 50 " pdb=" OP2 G D 52 " model vdw 2.239 3.040 ... (remaining 65773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.040 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.002 0.057 8893 Z= 0.144 Angle : 0.609 6.551 12540 Z= 0.329 Chirality : 0.067 0.256 1494 Planarity : 0.003 0.048 1322 Dihedral : 13.464 88.022 3265 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.81 % Allowed : 3.57 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.46 (0.24), residues: 934 helix: -1.57 (0.25), residues: 325 sheet: -4.91 (0.29), residues: 116 loop : -3.53 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 284 TYR 0.004 0.000 TYR A 501 PHE 0.007 0.000 PHE A 227 TRP 0.013 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 ( 8893) covalent geometry : angle 0.60868 / 0.33 (12540) hydrogen bonds : bond 0.13709 / 8.91 ( 348) hydrogen bonds : angle 5.58105 / 3.93 ( 877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 ILE cc_start: 0.8345 (mt) cc_final: 0.7330 (mt) REVERT: B 401 TRP cc_start: 0.8317 (m100) cc_final: 0.8098 (m100) outliers start: 5 outliers final: 4 residues processed: 154 average time/residue: 0.1140 time to fit residues: 22.6817 Evaluate side-chains 72 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS A 147 ASN A 478 GLN A 519 ASN B 57 ASN B 198 HIS B 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.085014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072343 restraints weight = 50782.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.073634 restraints weight = 29756.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.074509 restraints weight = 20079.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.075045 restraints weight = 15207.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.075474 restraints weight = 12630.343| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8893 Z= 0.127 Angle : 0.630 7.033 12540 Z= 0.289 Chirality : 0.049 0.169 1494 Planarity : 0.004 0.040 1322 Dihedral : 11.327 68.361 1887 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.55 (0.25), residues: 934 helix: -0.83 (0.27), residues: 336 sheet: -4.32 (0.31), residues: 131 loop : -2.96 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 83 TYR 0.012 0.001 TYR A 188 PHE 0.020 0.003 PHE B 130 TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8893) covalent geometry : angle 0.63023 / 0.29 (12540) hydrogen bonds : bond 0.03883 / 2.51 ( 348) hydrogen bonds : angle 4.49992 / 3.25 ( 877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8908 (pp30) cc_final: 0.8495 (pp30) REVERT: A 364 ASP cc_start: 0.8225 (p0) cc_final: 0.7462 (p0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0770 time to fit residues: 10.3101 Evaluate side-chains 56 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [53, 76, 64, 97, 22, 18, 85, 6, 94, 30, 12] chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 394 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS B 265 ASN B 330 GLN B 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.080338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.067198 restraints weight = 50846.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068388 restraints weight = 30271.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069201 restraints weight = 20864.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069745 restraints weight = 15972.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069998 restraints weight = 13308.741| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8893 Z= 0.227 Angle : 0.723 7.191 12540 Z= 0.342 Chirality : 0.051 0.195 1494 Planarity : 0.005 0.048 1322 Dihedral : 11.335 69.612 1887 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.41 (0.25), residues: 934 helix: -0.61 (0.28), residues: 339 sheet: -4.00 (0.29), residues: 165 loop : -2.89 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 143 TYR 0.022 0.003 TYR B 405 PHE 0.022 0.002 PHE A 160 TRP 0.029 0.002 TRP A 88 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 8893) covalent geometry : angle 0.72347 / 0.34 (12540) hydrogen bonds : bond 0.04476 / 2.91 ( 348) hydrogen bonds : angle 4.49612 / 3.29 ( 877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8301 (m-80) cc_final: 0.8057 (m-80) REVERT: A 182 GLN cc_start: 0.8894 (pp30) cc_final: 0.8440 (pp30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0709 time to fit residues: 7.5426 Evaluate side-chains 48 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [12, 90, 25, 15, 7, 52, 33, 76, 98, 17, 97] chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 97 optimal weight: 20.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.079643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066748 restraints weight = 51704.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067710 restraints weight = 32033.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068414 restraints weight = 21894.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068616 restraints weight = 17222.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.068697 restraints weight = 16379.467| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8893 Z= 0.172 Angle : 0.657 6.617 12540 Z= 0.308 Chirality : 0.049 0.226 1494 Planarity : 0.004 0.048 1322 Dihedral : 11.144 70.738 1887 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.81 (0.26), residues: 934 helix: -0.18 (0.29), residues: 328 sheet: -3.47 (0.32), residues: 164 loop : -2.51 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 557 TYR 0.018 0.002 TYR A 181 PHE 0.017 0.002 PHE A 227 TRP 0.016 0.002 TRP A 402 HIS 0.005 0.002 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8893) covalent geometry : angle 0.65710 / 0.31 (12540) hydrogen bonds : bond 0.03823 / 2.49 ( 348) hydrogen bonds : angle 4.32719 / 3.16 ( 877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8882 (pp30) cc_final: 0.8477 (pp30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0619 time to fit residues: 6.7378 Evaluate side-chains 44 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [37, 27, 17, 52, 44, 6, 46, 59, 82, 13, 16] chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 361 HIS B 145 GLN B 182 GLN B 265 ASN B 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.080878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067684 restraints weight = 50698.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068882 restraints weight = 29958.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069714 restraints weight = 20707.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070288 restraints weight = 15819.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070598 restraints weight = 13122.408| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8893 Z= 0.110 Angle : 0.597 6.603 12540 Z= 0.277 Chirality : 0.047 0.222 1494 Planarity : 0.004 0.038 1322 Dihedral : 10.999 69.434 1887 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.39 (0.27), residues: 934 helix: 0.10 (0.30), residues: 329 sheet: -3.09 (0.34), residues: 164 loop : -2.30 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 199 TYR 0.021 0.001 TYR B 146 PHE 0.016 0.002 PHE A 87 TRP 0.018 0.001 TRP A 402 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8893) covalent geometry : angle 0.59745 / 0.28 (12540) hydrogen bonds : bond 0.03541 / 2.28 ( 348) hydrogen bonds : angle 4.14675 / 3.00 ( 877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8860 (pp30) cc_final: 0.8551 (pp30) REVERT: A 409 THR cc_start: 0.9244 (p) cc_final: 0.9041 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0624 time to fit residues: 8.1211 Evaluate side-chains 50 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [92, 4, 30, 51, 37, 40, 94, 86, 27, 53, 43] chunk 92 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.079019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065804 restraints weight = 50759.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066958 restraints weight = 30138.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067728 restraints weight = 20690.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068245 restraints weight = 15906.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.068597 restraints weight = 13282.974| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8893 Z= 0.168 Angle : 0.654 6.595 12540 Z= 0.307 Chirality : 0.049 0.226 1494 Planarity : 0.004 0.037 1322 Dihedral : 11.124 69.087 1887 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.38 (0.27), residues: 934 helix: -0.01 (0.29), residues: 329 sheet: -2.97 (0.35), residues: 158 loop : -2.24 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 199 TYR 0.018 0.002 TYR B 405 PHE 0.018 0.002 PHE A 160 TRP 0.033 0.002 TRP B 426 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 8893) covalent geometry : angle 0.65407 / 0.31 (12540) hydrogen bonds : bond 0.03963 / 2.53 ( 348) hydrogen bonds : angle 4.28863 / 3.11 ( 877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8859 (pp30) cc_final: 0.8454 (pp30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0722 time to fit residues: 7.4387 Evaluate side-chains 40 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [92, 32, 80, 56, 23, 19, 14, 50, 7, 61, 74] chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 56 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.079265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066108 restraints weight = 51135.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.067287 restraints weight = 29998.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068069 restraints weight = 20589.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068541 restraints weight = 15866.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068927 restraints weight = 13438.488| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8893 Z= 0.127 Angle : 0.617 7.196 12540 Z= 0.285 Chirality : 0.048 0.215 1494 Planarity : 0.004 0.041 1322 Dihedral : 11.054 67.905 1887 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.18 (0.27), residues: 934 helix: 0.12 (0.29), residues: 329 sheet: -2.77 (0.36), residues: 160 loop : -2.14 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.013 0.001 TYR B 405 PHE 0.015 0.002 PHE A 227 TRP 0.031 0.001 TRP B 426 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8893) covalent geometry : angle 0.61688 / 0.28 (12540) hydrogen bonds : bond 0.03750 / 2.35 ( 348) hydrogen bonds : angle 4.20827 / 3.05 ( 877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8861 (pp30) cc_final: 0.8453 (pp30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0663 time to fit residues: 6.8838 Evaluate side-chains 42 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [57, 42, 16, 24, 12, 13, 38, 85, 35, 87, 5] chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS B 265 ASN B 373 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.078854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065650 restraints weight = 50556.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066783 restraints weight = 30026.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067570 restraints weight = 20853.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068071 restraints weight = 16087.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.068441 restraints weight = 13522.627| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8893 Z= 0.146 Angle : 0.625 6.482 12540 Z= 0.289 Chirality : 0.048 0.196 1494 Planarity : 0.004 0.040 1322 Dihedral : 11.092 67.138 1887 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.00 (0.27), residues: 934 helix: 0.27 (0.30), residues: 328 sheet: -2.57 (0.37), residues: 157 loop : -2.07 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.016 0.002 TYR B 405 PHE 0.018 0.002 PHE B 160 TRP 0.033 0.002 TRP B 426 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 8893) covalent geometry : angle 0.62518 / 0.29 (12540) hydrogen bonds : bond 0.03830 / 2.40 ( 348) hydrogen bonds : angle 4.14430 / 3.02 ( 877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8181 (m-80) cc_final: 0.7972 (m-80) REVERT: A 182 GLN cc_start: 0.8843 (pp30) cc_final: 0.8452 (pp30) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0641 time to fit residues: 6.4971 Evaluate side-chains 43 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [40, 69, 27, 1, 44, 20, 78, 18, 41, 8, 43] chunk 40 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.078005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064760 restraints weight = 50977.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065886 restraints weight = 30403.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066628 restraints weight = 21073.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067120 restraints weight = 16394.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.067389 restraints weight = 13829.533| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8893 Z= 0.188 Angle : 0.677 6.587 12540 Z= 0.317 Chirality : 0.049 0.187 1494 Planarity : 0.004 0.035 1322 Dihedral : 11.198 67.853 1887 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.11 (0.27), residues: 934 helix: 0.12 (0.29), residues: 330 sheet: -2.60 (0.37), residues: 163 loop : -2.09 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 557 TYR 0.022 0.002 TYR B 405 PHE 0.019 0.002 PHE A 227 TRP 0.025 0.002 TRP B 426 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 8893) covalent geometry : angle 0.67684 / 0.32 (12540) hydrogen bonds : bond 0.04194 / 2.66 ( 348) hydrogen bonds : angle 4.29698 / 3.13 ( 877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8331 (m-80) cc_final: 0.8063 (m-80) REVERT: A 182 GLN cc_start: 0.8841 (pp30) cc_final: 0.8464 (pp30) REVERT: B 369 THR cc_start: 0.9080 (p) cc_final: 0.8746 (t) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0674 time to fit residues: 6.4720 Evaluate side-chains 41 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [77, 20, 76, 70, 1, 54, 10, 16, 52, 15, 48] chunk 77 optimal weight: 0.0770 chunk 20 optimal weight: 0.0170 chunk 76 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.079907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066674 restraints weight = 50087.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067835 restraints weight = 29891.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.068624 restraints weight = 20671.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069101 restraints weight = 15919.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.069509 restraints weight = 13469.618| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8893 Z= 0.104 Angle : 0.617 6.224 12540 Z= 0.284 Chirality : 0.047 0.164 1494 Planarity : 0.004 0.032 1322 Dihedral : 10.944 67.309 1887 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.62 (0.28), residues: 934 helix: 0.44 (0.30), residues: 325 sheet: -2.23 (0.38), residues: 159 loop : -1.76 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.017 0.001 TYR A 188 PHE 0.018 0.002 PHE B 124 TRP 0.025 0.001 TRP A 402 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 8893) covalent geometry : angle 0.61656 / 0.28 (12540) hydrogen bonds : bond 0.03750 / 2.34 ( 348) hydrogen bonds : angle 4.14257 / 2.97 ( 877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8814 (pp30) cc_final: 0.8459 (pp30) REVERT: A 364 ASP cc_start: 0.8066 (p0) cc_final: 0.7620 (p0) REVERT: A 367 GLN cc_start: 0.8621 (mp10) cc_final: 0.8351 (mp10) REVERT: B 369 THR cc_start: 0.8951 (p) cc_final: 0.8592 (t) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0745 time to fit residues: 8.1815 Evaluate side-chains 51 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: [98, 100, 1, 17, 27, 54, 75, 96, 12, 89, 63] chunk 98 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.077540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064157 restraints weight = 50420.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065266 restraints weight = 30327.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066009 restraints weight = 21158.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066500 restraints weight = 16457.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066729 restraints weight = 13908.809| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8893 Z= 0.208 Angle : 0.697 6.472 12540 Z= 0.326 Chirality : 0.050 0.173 1494 Planarity : 0.004 0.032 1322 Dihedral : 11.165 68.208 1887 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.92 (0.28), residues: 934 helix: 0.18 (0.30), residues: 330 sheet: -2.23 (0.38), residues: 168 loop : -2.00 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 78 TYR 0.025 0.002 TYR B 405 PHE 0.022 0.002 PHE A 160 TRP 0.025 0.002 TRP B 426 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 8893) covalent geometry : angle 0.69669 / 0.33 (12540) hydrogen bonds : bond 0.04384 / 2.77 ( 348) hydrogen bonds : angle 4.32964 / 3.14 ( 877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1303.49 seconds wall clock time: 23 minutes 13.72 seconds (1393.72 seconds total)