Starting phenix.real_space_refine on Fri Sep 11 09:28:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.cif" model { file = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6waz_21582/09_2026/6waz_21582.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 8 5.16 5 C 5338 2.51 5 N 1453 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8537 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4222 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 21, 'TRP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3177 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 5, 'GLN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 493 Classifications: {'RNAv2': 23} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 22} 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: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 645 Classifications: {'DNA': 2, 'RNAv2': 29} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 17} Link IDs: {'rna3p': 30} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.45, per 1000 atoms: 0.17 Number of scatterers: 8537 At special positions: 0 Unit cell: (103.88, 116.6, 110.24, 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 8 16.00 P 51 15.00 O 1687 8.00 N 1453 7.00 C 5338 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: 0.79 Conformation dependent library (CDL) restraints added in 279.7 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.9% alpha, 9.0% beta 26 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 4.367A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.903A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.715A pdb=" N THR A 128 " --> pdb=" O ARG A 125 " (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 Processing helix chain 'A' and resid 253 through 269 removed outlier: 4.039A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.283A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 removed outlier: 3.764A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.552A pdb=" N TRP A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.935A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.610A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.824A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.934A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 6.184A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.742A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 155 through 175 removed outlier: 4.884A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.896A pdb=" N LYS B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.549A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 removed outlier: 3.564A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 394 through 406 removed outlier: 4.094A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 406 " --> pdb=" O TRP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.754A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 108 removed outlier: 3.682A pdb=" N VAL A 189 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.098A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 468 removed outlier: 3.624A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 493 " --> pdb=" O TYR A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.991A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 144 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.680A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.514A 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 removed outlier: 3.652A pdb=" N TYR B 188 " --> pdb=" O TYR B 181 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B 181 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.570A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 234 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 351 removed outlier: 7.327A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.801A pdb=" N GLY B 333 " --> pdb=" O GLN B 336 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.30 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: 1.21 - 1.33: 1771 1.33 - 1.45: 2201 1.45 - 1.57: 4786 1.57 - 1.69: 102 1.69 - 1.81: 13 Bond restraints: 8873 Sorted by residual: bond pdb=" CB THR B 131 " pdb=" CG2 THR B 131 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.50e+00 bond pdb=" C2' DC D 77 " pdb=" C1' DC D 77 " ideal model delta sigma weight residual 1.518 1.537 -0.019 1.00e-02 1.00e+04 3.78e+00 bond pdb=" CG GLU A 194 " pdb=" CD GLU A 194 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.36e+00 bond pdb=" CG1 ILE B 380 " pdb=" CD1 ILE B 380 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.89e+00 bond pdb=" CG ASP A 86 " pdb=" OD2 ASP A 86 " ideal model delta sigma weight residual 1.249 1.217 0.032 1.90e-02 2.77e+03 2.80e+00 ... (remaining 8868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11695 1.67 - 3.33: 545 3.33 - 5.00: 92 5.00 - 6.66: 19 6.66 - 8.33: 7 Bond angle restraints: 12358 Sorted by residual: angle pdb=" O4' DC D 77 " pdb=" C4' DC D 77 " pdb=" C3' DC D 77 " ideal model delta sigma weight residual 106.00 103.62 2.38 6.00e-01 2.78e+00 1.57e+01 angle pdb=" N ASP B 177 " pdb=" CA ASP B 177 " pdb=" C ASP B 177 " ideal model delta sigma weight residual 110.80 119.08 -8.28 2.13e+00 2.20e-01 1.51e+01 angle pdb=" N LYS A 431 " pdb=" CA LYS A 431 " pdb=" C LYS A 431 " ideal model delta sigma weight residual 112.92 108.63 4.29 1.23e+00 6.61e-01 1.21e+01 angle pdb=" CA GLU B 42 " pdb=" CB GLU B 42 " pdb=" CG GLU B 42 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA THR A 240 " pdb=" CB THR A 240 " pdb=" CG2 THR A 240 " ideal model delta sigma weight residual 110.50 116.09 -5.59 1.70e+00 3.46e-01 1.08e+01 ... (remaining 12353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4554 17.43 - 34.87: 408 34.87 - 52.30: 129 52.30 - 69.73: 39 69.73 - 87.16: 15 Dihedral angle restraints: 5145 sinusoidal: 2358 harmonic: 2787 Sorted by residual: dihedral pdb=" O5' C C 199 " pdb=" C5' C C 199 " pdb=" C4' C C 199 " pdb=" C3' C C 199 " ideal model delta sinusoidal sigma weight residual 180.00 126.38 53.62 3 6.40e+00 2.44e-02 5.06e+01 dihedral pdb=" O5' A C 192 " pdb=" C5' A C 192 " pdb=" C4' A C 192 " pdb=" C3' A C 192 " ideal model delta sinusoidal sigma weight residual 180.00 132.65 47.35 3 6.40e+00 2.44e-02 4.66e+01 dihedral pdb=" O5' U C 201 " pdb=" C5' U C 201 " pdb=" C4' U C 201 " pdb=" C3' U C 201 " ideal model delta sinusoidal sigma weight residual 60.00 106.46 -46.46 3 6.40e+00 2.44e-02 4.58e+01 ... (remaining 5142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1208 0.077 - 0.153: 143 0.153 - 0.230: 23 0.230 - 0.307: 59 0.307 - 0.383: 4 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CG LEU A 491 " pdb=" CB LEU A 491 " pdb=" CD1 LEU A 491 " pdb=" CD2 LEU A 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CB VAL B 261 " pdb=" CA VAL B 261 " pdb=" CG1 VAL B 261 " pdb=" CG2 VAL B 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL A 423 " pdb=" CA VAL A 423 " pdb=" CG1 VAL A 423 " pdb=" CG2 VAL A 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1434 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 194 " 0.014 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" CD GLU A 194 " -0.050 2.00e-02 2.50e+03 pdb=" OE1 GLU A 194 " 0.018 2.00e-02 2.50e+03 pdb=" OE2 GLU A 194 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 300 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C GLU A 300 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU A 300 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 301 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 370 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" CD GLU A 370 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 370 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 370 " -0.013 2.00e-02 2.50e+03 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 51 2.52 - 3.12: 6402 3.12 - 3.71: 13680 3.71 - 4.31: 17409 4.31 - 4.90: 27770 Nonbonded interactions: 65312 Sorted by model distance: nonbonded pdb=" O ASP B 177 " pdb=" OD1 ASP B 177 " model vdw 1.931 3.040 nonbonded pdb=" O THR A 215 " pdb=" OG1 THR A 216 " model vdw 2.127 3.040 nonbonded pdb=" O PHE A 61 " pdb=" CD2 LEU A 74 " model vdw 2.207 3.460 nonbonded pdb=" OG SER B 379 " pdb=" O LYS B 385 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU A 492 " pdb=" OE2 GLU A 529 " model vdw 2.237 3.040 ... (remaining 65307 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: 0.990 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.004 0.070 8873 Z= 0.192 Angle : 0.834 8.330 12358 Z= 0.436 Chirality : 0.074 0.383 1437 Planarity : 0.005 0.050 1358 Dihedral : 15.868 87.163 3347 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.27 % Allowed : 5.08 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.73 (0.22), residues: 945 helix: -2.19 (0.23), residues: 310 sheet: -3.76 (0.43), residues: 93 loop : -3.78 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 206 TYR 0.013 0.001 TYR B 339 PHE 0.017 0.002 PHE B 416 TRP 0.019 0.001 TRP A 402 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 8873) covalent geometry : angle 0.83381 / 0.44 (12358) hydrogen bonds : bond 0.13300 / 9.34 ( 329) hydrogen bonds : angle 6.47094 / 4.33 ( 839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.7908 (t80) cc_final: 0.7656 (t80) REVERT: A 181 TYR cc_start: 0.7803 (m-10) cc_final: 0.6386 (m-10) REVERT: A 246 LEU cc_start: 0.8618 (tp) cc_final: 0.8357 (tp) REVERT: A 373 GLN cc_start: 0.8584 (pp30) cc_final: 0.8256 (tm-30) REVERT: A 524 GLN cc_start: 0.8040 (tt0) cc_final: 0.7661 (tt0) REVERT: A 552 VAL cc_start: 0.9119 (m) cc_final: 0.8883 (t) REVERT: B 75 VAL cc_start: 0.8919 (t) cc_final: 0.8694 (t) REVERT: B 254 VAL cc_start: 0.8808 (t) cc_final: 0.7895 (t) REVERT: B 258 GLN cc_start: 0.8897 (mt0) cc_final: 0.8690 (mp10) REVERT: B 318 TYR cc_start: 0.7723 (m-80) cc_final: 0.7132 (m-80) REVERT: B 395 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8176 (ttpt) REVERT: B 405 TYR cc_start: 0.7679 (m-80) cc_final: 0.7173 (m-80) outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.1049 time to fit residues: 24.4792 Evaluate side-chains 95 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 315 HIS A 394 GLN A 475 GLN A 507 GLN A 524 GLN A 547 GLN B 145 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079755 restraints weight = 25430.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.081689 restraints weight = 13646.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082976 restraints weight = 8724.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083833 restraints weight = 6311.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084344 restraints weight = 5030.077| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8873 Z= 0.175 Angle : 0.742 7.313 12358 Z= 0.347 Chirality : 0.049 0.185 1437 Planarity : 0.005 0.051 1358 Dihedral : 11.967 73.236 1633 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.49 (0.25), residues: 945 helix: -0.70 (0.28), residues: 312 sheet: -3.34 (0.45), residues: 98 loop : -3.28 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.016 0.002 TYR A 232 PHE 0.017 0.002 PHE A 171 TRP 0.021 0.001 TRP A 402 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 8873) covalent geometry : angle 0.74209 / 0.35 (12358) hydrogen bonds : bond 0.03931 / 2.65 ( 329) hydrogen bonds : angle 4.76549 / 3.19 ( 839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.8019 (m-10) cc_final: 0.6592 (m-10) REVERT: A 246 LEU cc_start: 0.8425 (tp) cc_final: 0.8055 (tt) REVERT: A 351 THR cc_start: 0.9411 (t) cc_final: 0.9036 (p) REVERT: A 524 GLN cc_start: 0.8212 (tt0) cc_final: 0.7789 (tt0) REVERT: A 552 VAL cc_start: 0.9078 (m) cc_final: 0.8797 (p) REVERT: B 75 VAL cc_start: 0.8949 (t) cc_final: 0.8602 (t) REVERT: B 254 VAL cc_start: 0.8912 (t) cc_final: 0.8042 (t) REVERT: B 318 TYR cc_start: 0.7866 (m-80) cc_final: 0.7207 (m-80) REVERT: B 395 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8489 (tptt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.0856 time to fit residues: 15.7742 Evaluate side-chains 85 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 40 optimal weight: 0.0370 chunk 82 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 332 GLN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.097723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081120 restraints weight = 24856.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.082894 restraints weight = 13793.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084072 restraints weight = 9024.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084855 restraints weight = 6647.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085326 restraints weight = 5374.991| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8873 Z= 0.125 Angle : 0.675 7.973 12358 Z= 0.314 Chirality : 0.047 0.143 1437 Planarity : 0.004 0.053 1358 Dihedral : 11.755 73.160 1633 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.27 % Allowed : 3.07 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 945 helix: -0.18 (0.29), residues: 312 sheet: -3.41 (0.41), residues: 119 loop : -2.90 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 277 TYR 0.013 0.001 TYR A 457 PHE 0.018 0.002 PHE A 171 TRP 0.020 0.001 TRP A 402 HIS 0.005 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8873) covalent geometry : angle 0.67518 / 0.31 (12358) hydrogen bonds : bond 0.03667 / 2.54 ( 329) hydrogen bonds : angle 4.42607 / 2.98 ( 839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: A 181 TYR cc_start: 0.8356 (m-10) cc_final: 0.7418 (m-10) REVERT: A 246 LEU cc_start: 0.8406 (tp) cc_final: 0.8073 (tt) REVERT: A 351 THR cc_start: 0.9355 (t) cc_final: 0.8997 (p) REVERT: A 358 ARG cc_start: 0.9067 (mmm-85) cc_final: 0.8812 (mmm160) REVERT: A 483 TYR cc_start: 0.8615 (t80) cc_final: 0.8260 (t80) REVERT: A 524 GLN cc_start: 0.8362 (tt0) cc_final: 0.7915 (tt0) REVERT: A 552 VAL cc_start: 0.9104 (m) cc_final: 0.8834 (p) REVERT: B 75 VAL cc_start: 0.8999 (t) cc_final: 0.8676 (t) REVERT: B 318 TYR cc_start: 0.7815 (m-80) cc_final: 0.7207 (m-80) REVERT: B 395 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8491 (tptt) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.0823 time to fit residues: 15.8294 Evaluate side-chains 91 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN B 255 ASN B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.096205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.079171 restraints weight = 25540.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080913 restraints weight = 14527.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082107 restraints weight = 9679.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082894 restraints weight = 7201.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083304 restraints weight = 5856.840| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8873 Z= 0.143 Angle : 0.664 7.184 12358 Z= 0.307 Chirality : 0.046 0.140 1437 Planarity : 0.004 0.053 1358 Dihedral : 11.538 73.099 1633 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.13 % Allowed : 4.14 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.68 (0.26), residues: 945 helix: 0.04 (0.29), residues: 316 sheet: -3.16 (0.41), residues: 128 loop : -2.69 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 277 TYR 0.018 0.001 TYR A 339 PHE 0.019 0.002 PHE A 171 TRP 0.019 0.001 TRP A 402 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8873) covalent geometry : angle 0.66395 / 0.31 (12358) hydrogen bonds : bond 0.03601 / 2.50 ( 329) hydrogen bonds : angle 4.31208 / 2.92 ( 839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8320 (mmp) cc_final: 0.8048 (mmm) REVERT: A 181 TYR cc_start: 0.8101 (m-10) cc_final: 0.7113 (m-10) REVERT: A 210 LEU cc_start: 0.8550 (tp) cc_final: 0.8171 (pp) REVERT: A 246 LEU cc_start: 0.8457 (tp) cc_final: 0.8029 (tt) REVERT: A 370 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8339 (mm-30) REVERT: A 483 TYR cc_start: 0.8725 (t80) cc_final: 0.8330 (t80) REVERT: A 524 GLN cc_start: 0.8332 (tt0) cc_final: 0.7978 (tt0) REVERT: A 552 VAL cc_start: 0.9110 (m) cc_final: 0.8856 (p) REVERT: B 318 TYR cc_start: 0.7810 (m-80) cc_final: 0.7195 (m-80) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.0856 time to fit residues: 14.7935 Evaluate side-chains 78 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.0010 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079098 restraints weight = 25081.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.081012 restraints weight = 13571.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082289 restraints weight = 8753.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083140 restraints weight = 6376.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.083688 restraints weight = 5118.911| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8873 Z= 0.120 Angle : 0.657 7.888 12358 Z= 0.302 Chirality : 0.046 0.134 1437 Planarity : 0.004 0.055 1358 Dihedral : 11.382 72.389 1633 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.46 (0.27), residues: 945 helix: 0.19 (0.29), residues: 323 sheet: -2.79 (0.43), residues: 127 loop : -2.65 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 277 TYR 0.025 0.001 TYR A 405 PHE 0.020 0.002 PHE A 171 TRP 0.025 0.001 TRP A 402 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8873) covalent geometry : angle 0.65656 / 0.30 (12358) hydrogen bonds : bond 0.03420 / 2.39 ( 329) hydrogen bonds : angle 4.17622 / 2.84 ( 839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8345 (mmp) cc_final: 0.8085 (mmm) REVERT: A 181 TYR cc_start: 0.8174 (m-10) cc_final: 0.7051 (m-10) REVERT: A 210 LEU cc_start: 0.8556 (tp) cc_final: 0.8153 (pp) REVERT: A 246 LEU cc_start: 0.8504 (tp) cc_final: 0.8098 (tt) REVERT: A 370 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 483 TYR cc_start: 0.8743 (t80) cc_final: 0.8454 (t80) REVERT: A 524 GLN cc_start: 0.8342 (tt0) cc_final: 0.7844 (tt0) REVERT: A 552 VAL cc_start: 0.9096 (m) cc_final: 0.8857 (p) REVERT: B 318 TYR cc_start: 0.7853 (m-80) cc_final: 0.7217 (m-80) REVERT: B 378 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7956 (tt0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0806 time to fit residues: 14.0388 Evaluate side-chains 81 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.094344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076815 restraints weight = 24909.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078694 restraints weight = 13596.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079939 restraints weight = 8787.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080754 restraints weight = 6412.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081257 restraints weight = 5147.840| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8873 Z= 0.160 Angle : 0.677 7.428 12358 Z= 0.315 Chirality : 0.047 0.163 1437 Planarity : 0.005 0.055 1358 Dihedral : 11.383 71.906 1633 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.24 (0.27), residues: 945 helix: 0.26 (0.30), residues: 324 sheet: -2.43 (0.46), residues: 117 loop : -2.53 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 277 TYR 0.019 0.001 TYR A 405 PHE 0.012 0.002 PHE A 227 TRP 0.026 0.002 TRP B 426 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8873) covalent geometry : angle 0.67653 / 0.32 (12358) hydrogen bonds : bond 0.03676 / 2.53 ( 329) hydrogen bonds : angle 4.22520 / 2.90 ( 839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8360 (mmp) cc_final: 0.8097 (mmm) REVERT: A 161 GLN cc_start: 0.7989 (pm20) cc_final: 0.7655 (pm20) REVERT: A 181 TYR cc_start: 0.8181 (m-10) cc_final: 0.7203 (m-10) REVERT: A 246 LEU cc_start: 0.8428 (tp) cc_final: 0.8073 (tt) REVERT: A 370 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8222 (tp30) REVERT: A 483 TYR cc_start: 0.8822 (t80) cc_final: 0.8527 (t80) REVERT: A 524 GLN cc_start: 0.8361 (tt0) cc_final: 0.7853 (tt0) REVERT: A 552 VAL cc_start: 0.9120 (m) cc_final: 0.8899 (p) REVERT: B 318 TYR cc_start: 0.7910 (m-80) cc_final: 0.7296 (m-80) REVERT: B 378 GLU cc_start: 0.8250 (mt-10) cc_final: 0.8014 (tt0) REVERT: B 426 TRP cc_start: 0.7676 (t60) cc_final: 0.7457 (t60) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0910 time to fit residues: 14.9419 Evaluate side-chains 79 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 475 GLN B 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077640 restraints weight = 25283.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079554 restraints weight = 13783.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.080848 restraints weight = 8911.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081699 restraints weight = 6486.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082224 restraints weight = 5192.028| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8873 Z= 0.113 Angle : 0.643 6.536 12358 Z= 0.295 Chirality : 0.046 0.134 1437 Planarity : 0.004 0.057 1358 Dihedral : 11.205 70.849 1633 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.91 (0.27), residues: 945 helix: 0.60 (0.30), residues: 324 sheet: -2.38 (0.45), residues: 127 loop : -2.33 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 277 TYR 0.016 0.001 TYR A 405 PHE 0.017 0.002 PHE A 171 TRP 0.031 0.001 TRP B 88 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8873) covalent geometry : angle 0.64348 / 0.30 (12358) hydrogen bonds : bond 0.03387 / 2.38 ( 329) hydrogen bonds : angle 4.05757 / 2.80 ( 839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8410 (mmp) cc_final: 0.8196 (mmm) REVERT: A 181 TYR cc_start: 0.8295 (m-10) cc_final: 0.7273 (m-10) REVERT: A 370 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8162 (tp30) REVERT: A 552 VAL cc_start: 0.9108 (m) cc_final: 0.8890 (p) REVERT: B 178 ILE cc_start: 0.9341 (mt) cc_final: 0.9086 (tt) REVERT: B 279 LEU cc_start: 0.8975 (mp) cc_final: 0.8632 (mt) REVERT: B 307 ARG cc_start: 0.8225 (mpp80) cc_final: 0.7797 (mtm-85) REVERT: B 378 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8012 (tt0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0781 time to fit residues: 13.2886 Evaluate side-chains 81 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 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 = 0.3332 r_free = 0.3332 target = 0.089025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.071294 restraints weight = 25903.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073058 restraints weight = 14235.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.074228 restraints weight = 9309.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.075015 restraints weight = 6902.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075514 restraints weight = 5606.849| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 8873 Z= 0.290 Angle : 0.827 8.930 12358 Z= 0.388 Chirality : 0.051 0.218 1437 Planarity : 0.005 0.052 1358 Dihedral : 11.622 71.148 1633 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 945 helix: 0.16 (0.29), residues: 327 sheet: -2.45 (0.47), residues: 107 loop : -2.41 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 211 TYR 0.022 0.003 TYR A 405 PHE 0.027 0.003 PHE B 171 TRP 0.047 0.003 TRP B 414 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.29 ( 8873) covalent geometry : angle 0.82694 / 0.39 (12358) hydrogen bonds : bond 0.04509 / 3.11 ( 329) hydrogen bonds : angle 4.40536 / 3.04 ( 839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8177 (pm20) cc_final: 0.7778 (pm20) REVERT: A 181 TYR cc_start: 0.8344 (m-10) cc_final: 0.7588 (m-10) REVERT: A 210 LEU cc_start: 0.8616 (tp) cc_final: 0.7984 (pp) REVERT: A 370 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8442 (tp30) REVERT: A 483 TYR cc_start: 0.8984 (t80) cc_final: 0.8323 (t80) REVERT: A 491 LEU cc_start: 0.8573 (tt) cc_final: 0.8366 (tt) REVERT: A 552 VAL cc_start: 0.9195 (m) cc_final: 0.8967 (p) REVERT: B 177 ASP cc_start: 0.8273 (p0) cc_final: 0.8039 (p0) REVERT: B 307 ARG cc_start: 0.8415 (mpp80) cc_final: 0.7957 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0877 time to fit residues: 12.7935 Evaluate side-chains 79 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.074502 restraints weight = 25539.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.076340 restraints weight = 14048.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077526 restraints weight = 9188.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078393 restraints weight = 6841.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.078959 restraints weight = 5514.277| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8873 Z= 0.126 Angle : 0.683 7.400 12358 Z= 0.315 Chirality : 0.047 0.156 1437 Planarity : 0.004 0.054 1358 Dihedral : 11.306 69.657 1633 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.81 (0.27), residues: 945 helix: 0.50 (0.30), residues: 322 sheet: -2.14 (0.46), residues: 118 loop : -2.18 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 211 TYR 0.014 0.001 TYR A 405 PHE 0.017 0.002 PHE B 130 TRP 0.031 0.002 TRP A 402 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8873) covalent geometry : angle 0.68299 / 0.31 (12358) hydrogen bonds : bond 0.03719 / 2.58 ( 329) hydrogen bonds : angle 4.19704 / 2.90 ( 839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.327 Fit side-chains REVERT: A 161 GLN cc_start: 0.7868 (pm20) cc_final: 0.7625 (pm20) REVERT: A 181 TYR cc_start: 0.8380 (m-10) cc_final: 0.7497 (m-10) REVERT: A 370 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 552 VAL cc_start: 0.9191 (m) cc_final: 0.8967 (p) REVERT: B 279 LEU cc_start: 0.9037 (mp) cc_final: 0.8693 (mt) REVERT: B 307 ARG cc_start: 0.8357 (mpp80) cc_final: 0.7988 (mtm-85) REVERT: B 395 LYS cc_start: 0.9296 (tptp) cc_final: 0.8892 (ttpt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0891 time to fit residues: 14.3976 Evaluate side-chains 83 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 0.0770 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075202 restraints weight = 25506.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.077083 restraints weight = 13917.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078297 restraints weight = 9028.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.079127 restraints weight = 6683.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079617 restraints weight = 5423.040| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8873 Z= 0.118 Angle : 0.669 6.714 12358 Z= 0.311 Chirality : 0.046 0.140 1437 Planarity : 0.004 0.055 1358 Dihedral : 11.160 69.490 1633 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.28), residues: 945 helix: 0.56 (0.30), residues: 326 sheet: -2.04 (0.45), residues: 128 loop : -2.02 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 211 TYR 0.012 0.001 TYR A 405 PHE 0.035 0.002 PHE A 171 TRP 0.032 0.002 TRP A 402 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8873) covalent geometry : angle 0.66899 / 0.31 (12358) hydrogen bonds : bond 0.03586 / 2.48 ( 329) hydrogen bonds : angle 4.24029 / 2.93 ( 839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.410 Fit side-chains REVERT: A 161 GLN cc_start: 0.7828 (pm20) cc_final: 0.7577 (pm20) REVERT: A 181 TYR cc_start: 0.8425 (m-10) cc_final: 0.7504 (m-10) REVERT: A 370 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8324 (tp30) REVERT: A 439 THR cc_start: 0.9546 (p) cc_final: 0.9244 (t) REVERT: A 552 VAL cc_start: 0.9150 (m) cc_final: 0.8935 (p) REVERT: B 34 LEU cc_start: 0.8562 (mt) cc_final: 0.8361 (mm) REVERT: B 279 LEU cc_start: 0.9028 (mp) cc_final: 0.8682 (mt) REVERT: B 307 ARG cc_start: 0.8425 (mpp80) cc_final: 0.8018 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0961 time to fit residues: 14.0857 Evaluate side-chains 81 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 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 = 0.3374 r_free = 0.3374 target = 0.091546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073739 restraints weight = 25383.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075537 restraints weight = 13825.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076756 restraints weight = 9037.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077505 restraints weight = 6672.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078065 restraints weight = 5452.676| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8873 Z= 0.175 Angle : 0.687 7.194 12358 Z= 0.320 Chirality : 0.047 0.155 1437 Planarity : 0.004 0.054 1358 Dihedral : 11.229 69.599 1633 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.66 (0.28), residues: 945 helix: 0.49 (0.30), residues: 325 sheet: -2.14 (0.44), residues: 131 loop : -1.95 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.013 0.001 TYR A 405 PHE 0.016 0.002 PHE B 171 TRP 0.032 0.002 TRP B 414 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 8873) covalent geometry : angle 0.68704 / 0.32 (12358) hydrogen bonds : bond 0.03809 / 2.62 ( 329) hydrogen bonds : angle 4.22636 / 2.92 ( 839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1310.24 seconds wall clock time: 23 minutes 26.01 seconds (1406.01 seconds total)