Starting phenix.real_space_refine on Tue Mar 3 21:32:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb0_21583/03_2026/6wb0_21583.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb0_21583/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6wb0_21583/03_2026/6wb0_21583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb0_21583/03_2026/6wb0_21583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wb0_21583/03_2026/6wb0_21583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb0_21583/03_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-dev-5986/lib/python3.9/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: {'RNA': 35} Modifications used: {'5*END': 1, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna3p': 34} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 881 Inner-chain residues flagged as termini: ['pdbres=" G D 46 "'] Classifications: {'DNA': 4, 'RNA': 38} Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.28, per 1000 atoms: 0.27 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: 0.81 Conformation dependent library (CDL) restraints added in 242.3 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: 1.11 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: 1.29 Time building geometry restraints manager: 1.02 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 1.337 1.361 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" C THR A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.326 1.341 -0.015 1.44e-02 4.82e+03 1.08e+00 bond pdb=" C GLU A 169 " pdb=" O GLU A 169 " ideal model delta sigma weight residual 1.241 1.231 0.010 9.80e-03 1.04e+04 1.07e+00 bond pdb=" CG PRO A 226 " pdb=" CD PRO A 226 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.03e+00 ... (remaining 8888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 12220 1.31 - 2.62: 240 2.62 - 3.93: 82 3.93 - 5.24: 4 5.24 - 6.55: 3 Bond angle restraints: 12549 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=" CA VAL A 467 " pdb=" C VAL A 467 " pdb=" N PRO A 468 " ideal model delta sigma weight residual 116.57 119.44 -2.87 9.80e-01 1.04e+00 8.61e+00 angle pdb=" N ILE B 180 " pdb=" CA ILE B 180 " pdb=" C ILE B 180 " ideal model delta sigma weight residual 108.48 112.47 -3.99 1.44e+00 4.82e-01 7.66e+00 angle pdb=" CA GLU A 169 " pdb=" C GLU A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 120.79 118.14 2.65 9.70e-01 1.06e+00 7.44e+00 angle pdb=" N LYS A 49 " pdb=" CA LYS A 49 " pdb=" C LYS A 49 " ideal model delta sigma weight residual 107.32 111.61 -4.29 1.65e+00 3.67e-01 6.75e+00 ... (remaining 12544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4820 17.60 - 35.21: 292 35.21 - 52.81: 116 52.81 - 70.42: 78 70.42 - 88.02: 27 Dihedral angle restraints: 5333 sinusoidal: 2572 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 -65.00 -7.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA LYS B 73 " pdb=" CB LYS B 73 " pdb=" CG LYS B 73 " pdb=" CD LYS B 73 " ideal model delta sinusoidal sigma weight residual 180.00 124.82 55.18 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N PHE B 61 " pdb=" CA PHE B 61 " pdb=" CB PHE B 61 " pdb=" CG PHE B 61 " ideal model delta sinusoidal sigma weight residual 60.00 4.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 5330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1176 0.037 - 0.074: 197 0.074 - 0.111: 84 0.111 - 0.148: 33 0.148 - 0.185: 4 Chirality restraints: 1494 Sorted by residual: 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 -2.66 -2.47 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C3' DG D 73 " pdb=" C4' DG D 73 " pdb=" O3' DG D 73 " pdb=" C2' DG D 73 " both_signs ideal model delta sigma weight residual False -2.66 -2.48 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C3' DC D 77 " pdb=" C4' DC D 77 " pdb=" O3' DC D 77 " pdb=" C2' DC D 77 " both_signs ideal model delta sigma weight residual False -2.66 -2.48 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (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: 1.200 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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= 0.119 Angle : 0.507 6.551 12549 Z= 0.289 Chirality : 0.039 0.185 1494 Planarity : 0.003 0.048 1322 Dihedral : 16.404 88.022 3547 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 covalent geometry : bond 0.00203 ( 8893) covalent geometry : angle 0.50652 (12549) hydrogen bonds : bond 0.13709 ( 348) hydrogen bonds : angle 5.58105 ( 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 : 0.288 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: 0.1161 time to fit residues: 22.9174 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 : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 147 ASN A 394 GLN A 478 GLN A 519 ASN B 57 ASN B 198 HIS B 265 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.084659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071914 restraints weight = 50694.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.073161 restraints weight = 29554.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074027 restraints weight = 20150.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.074503 restraints weight = 15240.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074972 restraints weight = 12768.891| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8893 Z= 0.117 Angle : 0.543 6.934 12549 Z= 0.266 Chirality : 0.040 0.185 1494 Planarity : 0.004 0.042 1322 Dihedral : 16.719 73.915 2169 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -3.39 (0.26), residues: 934 helix: -0.67 (0.28), residues: 338 sheet: -4.26 (0.30), residues: 137 loop : -2.84 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 83 TYR 0.013 0.001 TYR A 188 PHE 0.015 0.002 PHE B 130 TRP 0.020 0.001 TRP A 402 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8893) covalent geometry : angle 0.54337 (12549) hydrogen bonds : bond 0.03582 ( 348) hydrogen bonds : angle 4.36185 ( 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 93 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8903 (pp30) cc_final: 0.8494 (pp30) REVERT: A 364 ASP cc_start: 0.8225 (p0) cc_final: 0.7340 (p0) REVERT: B 271 TYR cc_start: 0.6826 (m-80) cc_final: 0.6586 (m-10) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0796 time to fit residues: 10.6868 Evaluate side-chains 55 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3691 r_free = 0.3691 target = 0.082598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069520 restraints weight = 50718.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070743 restraints weight = 29719.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071599 restraints weight = 20406.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.072125 restraints weight = 15531.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072533 restraints weight = 12980.074| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2591 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= 0.137 Angle : 0.529 6.888 12549 Z= 0.267 Chirality : 0.039 0.151 1494 Planarity : 0.004 0.048 1322 Dihedral : 16.792 74.223 2169 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -2.99 (0.26), residues: 934 helix: -0.31 (0.29), residues: 337 sheet: -3.79 (0.30), residues: 155 loop : -2.63 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.022 0.001 TYR A 483 PHE 0.015 0.002 PHE A 160 TRP 0.019 0.001 TRP B 426 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8893) covalent geometry : angle 0.52920 (12549) hydrogen bonds : bond 0.03508 ( 348) hydrogen bonds : angle 4.23574 ( 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 79 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8453 (tpp) cc_final: 0.8238 (tpp) REVERT: A 182 GLN cc_start: 0.8848 (pp30) cc_final: 0.8536 (pp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0651 time to fit residues: 7.8502 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 : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 145 GLN B 182 GLN B 198 HIS 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 = 0.3630 r_free = 0.3630 target = 0.079819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066482 restraints weight = 51761.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067679 restraints weight = 30275.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068482 restraints weight = 20734.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.068971 restraints weight = 15949.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069350 restraints weight = 13442.902| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3365 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= 0.144 Angle : 0.542 6.583 12549 Z= 0.273 Chirality : 0.040 0.159 1494 Planarity : 0.004 0.053 1322 Dihedral : 16.975 74.309 2169 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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: -2.60 (0.27), residues: 934 helix: -0.17 (0.29), residues: 334 sheet: -3.31 (0.32), residues: 165 loop : -2.29 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 211 TYR 0.017 0.002 TYR A 188 PHE 0.015 0.002 PHE A 160 TRP 0.018 0.002 TRP B 426 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8893) covalent geometry : angle 0.54190 (12549) hydrogen bonds : bond 0.03542 ( 348) hydrogen bonds : angle 4.06615 ( 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 74 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8822 (pp30) cc_final: 0.8532 (pp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0642 time to fit residues: 7.1921 Evaluate side-chains 46 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.0020 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 330 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.080541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067268 restraints weight = 50777.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068448 restraints weight = 29868.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069275 restraints weight = 20517.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069839 restraints weight = 15636.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.070145 restraints weight = 12983.741| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8893 Z= 0.105 Angle : 0.511 6.490 12549 Z= 0.255 Chirality : 0.039 0.153 1494 Planarity : 0.004 0.044 1322 Dihedral : 16.962 74.151 2169 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.19 (0.27), residues: 934 helix: 0.16 (0.30), residues: 329 sheet: -2.91 (0.35), residues: 154 loop : -2.15 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.015 0.001 TYR A 483 PHE 0.014 0.001 PHE A 227 TRP 0.021 0.001 TRP B 426 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8893) covalent geometry : angle 0.51077 (12549) hydrogen bonds : bond 0.03402 ( 348) hydrogen bonds : angle 4.04904 ( 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 74 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8814 (pp30) cc_final: 0.8428 (pp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0665 time to fit residues: 7.7207 Evaluate side-chains 47 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.066595 restraints weight = 50391.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067759 restraints weight = 30003.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068545 restraints weight = 20718.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069068 restraints weight = 16032.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069345 restraints weight = 13463.480| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8893 Z= 0.125 Angle : 0.519 6.783 12549 Z= 0.259 Chirality : 0.039 0.163 1494 Planarity : 0.004 0.039 1322 Dihedral : 17.022 74.232 2169 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -2.00 (0.27), residues: 934 helix: 0.23 (0.30), residues: 331 sheet: -2.69 (0.36), residues: 160 loop : -1.98 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 211 TYR 0.015 0.001 TYR A 188 PHE 0.013 0.001 PHE A 160 TRP 0.016 0.001 TRP B 426 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8893) covalent geometry : angle 0.51923 (12549) hydrogen bonds : bond 0.03594 ( 348) hydrogen bonds : angle 4.07984 ( 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 : 0.287 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8840 (pp30) cc_final: 0.8444 (pp30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0637 time to fit residues: 6.7763 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.080682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067418 restraints weight = 50788.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068598 restraints weight = 30037.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069401 restraints weight = 20669.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.069949 restraints weight = 15866.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070271 restraints weight = 13195.903| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8893 Z= 0.094 Angle : 0.506 6.313 12549 Z= 0.250 Chirality : 0.038 0.164 1494 Planarity : 0.004 0.037 1322 Dihedral : 16.949 74.076 2169 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -1.74 (0.28), residues: 934 helix: 0.40 (0.30), residues: 333 sheet: -2.43 (0.37), residues: 160 loop : -1.86 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 199 TYR 0.010 0.001 TYR A 483 PHE 0.012 0.001 PHE A 227 TRP 0.030 0.001 TRP B 401 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8893) covalent geometry : angle 0.50594 (12549) hydrogen bonds : bond 0.03380 ( 348) hydrogen bonds : angle 4.02881 ( 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 68 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8797 (pp30) cc_final: 0.8395 (pp30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0660 time to fit residues: 6.8581 Evaluate side-chains 45 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.078650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065329 restraints weight = 50516.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066450 restraints weight = 30259.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.067227 restraints weight = 21201.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067726 restraints weight = 16464.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068046 restraints weight = 13882.325| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8893 Z= 0.158 Angle : 0.556 6.305 12549 Z= 0.281 Chirality : 0.039 0.151 1494 Planarity : 0.004 0.058 1322 Dihedral : 17.119 74.332 2169 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -1.85 (0.28), residues: 934 helix: 0.28 (0.29), residues: 333 sheet: -2.43 (0.36), residues: 171 loop : -1.88 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 307 TYR 0.020 0.002 TYR B 405 PHE 0.018 0.002 PHE A 160 TRP 0.027 0.002 TRP B 401 HIS 0.002 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8893) covalent geometry : angle 0.55629 (12549) hydrogen bonds : bond 0.03976 ( 348) hydrogen bonds : angle 4.16036 ( 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 62 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8831 (pp30) cc_final: 0.8415 (pp30) REVERT: A 364 ASP cc_start: 0.7955 (p0) cc_final: 0.7351 (p0) REVERT: A 367 GLN cc_start: 0.8528 (mp10) cc_final: 0.8156 (mp10) REVERT: A 409 THR cc_start: 0.9373 (p) cc_final: 0.9130 (t) REVERT: A 493 VAL cc_start: 0.8622 (p) cc_final: 0.8291 (t) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0646 time to fit residues: 6.3758 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 44 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063451 restraints weight = 51148.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064575 restraints weight = 30802.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065302 restraints weight = 21483.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065723 restraints weight = 16811.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066098 restraints weight = 14431.517| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8893 Z= 0.207 Angle : 0.620 6.284 12549 Z= 0.319 Chirality : 0.041 0.148 1494 Planarity : 0.005 0.053 1322 Dihedral : 17.398 74.478 2169 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -1.90 (0.27), residues: 934 helix: 0.11 (0.29), residues: 323 sheet: -2.32 (0.38), residues: 165 loop : -1.84 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 199 TYR 0.028 0.002 TYR B 405 PHE 0.025 0.003 PHE B 124 TRP 0.029 0.002 TRP B 426 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8893) covalent geometry : angle 0.61967 (12549) hydrogen bonds : bond 0.04478 ( 348) hydrogen bonds : angle 4.37727 ( 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 53 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8910 (pp30) cc_final: 0.8455 (pp30) REVERT: A 364 ASP cc_start: 0.8110 (p0) cc_final: 0.7648 (p0) REVERT: A 367 GLN cc_start: 0.8463 (mp10) cc_final: 0.8192 (mp10) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0704 time to fit residues: 5.5552 Evaluate side-chains 39 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.078842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065652 restraints weight = 50113.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066787 restraints weight = 29754.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067550 restraints weight = 20635.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068071 restraints weight = 16006.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068298 restraints weight = 13510.834| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8893 Z= 0.103 Angle : 0.531 8.303 12549 Z= 0.263 Chirality : 0.038 0.152 1494 Planarity : 0.004 0.048 1322 Dihedral : 17.096 74.137 2169 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.46 (0.28), residues: 934 helix: 0.45 (0.30), residues: 326 sheet: -2.07 (0.39), residues: 159 loop : -1.58 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.015 0.001 TYR A 188 PHE 0.017 0.002 PHE A 87 TRP 0.019 0.001 TRP A 402 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8893) covalent geometry : angle 0.53105 (12549) hydrogen bonds : bond 0.03817 ( 348) hydrogen bonds : angle 4.12602 ( 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 66 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8602 (m-80) cc_final: 0.8356 (m-80) REVERT: A 182 GLN cc_start: 0.8883 (pp30) cc_final: 0.8426 (pp30) REVERT: A 364 ASP cc_start: 0.8187 (p0) cc_final: 0.7559 (p0) REVERT: A 367 GLN cc_start: 0.8665 (mp10) cc_final: 0.8391 (mp10) REVERT: A 409 THR cc_start: 0.9410 (p) cc_final: 0.9142 (t) REVERT: A 493 VAL cc_start: 0.8638 (p) cc_final: 0.8314 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0765 time to fit residues: 7.3488 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063994 restraints weight = 50829.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065127 restraints weight = 30308.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065866 restraints weight = 20948.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.066342 restraints weight = 16252.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066702 restraints weight = 13799.875| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8893 Z= 0.177 Angle : 0.583 6.415 12549 Z= 0.292 Chirality : 0.040 0.147 1494 Planarity : 0.004 0.051 1322 Dihedral : 17.227 74.328 2169 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % 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: -1.69 (0.28), residues: 934 helix: 0.27 (0.29), residues: 333 sheet: -2.22 (0.38), residues: 171 loop : -1.72 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.027 0.002 TYR B 115 PHE 0.018 0.002 PHE A 160 TRP 0.050 0.002 TRP B 401 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8893) covalent geometry : angle 0.58280 (12549) hydrogen bonds : bond 0.04300 ( 348) hydrogen bonds : angle 4.19507 ( 877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.11 seconds wall clock time: 22 minutes 34.71 seconds (1354.71 seconds total)