Starting phenix.real_space_refine on Thu Jul 2 21:20:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ply_13506/07_2026/7ply_13506.cif" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6471 2.51 5 N 1720 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 10149 At special positions: 0 Unit cell: (106.7, 132, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1891 8.00 N 1720 7.00 C 6471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 355.8 milliseconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.956A pdb=" N ILE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.683A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.321A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.255A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 4.127A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.114A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.741A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.549A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.620A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.526A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.581A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.195A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 127 removed outlier: 4.097A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.543A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.745A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.028A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.216A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 50 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 7.669A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 5.033A pdb=" N SER A 342 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA A 349 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 344 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.599A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.856A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 529 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2903 1.33 - 1.46: 2846 1.46 - 1.60: 4514 1.60 - 1.73: 0 1.73 - 1.86: 102 Bond restraints: 10365 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.502 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.501 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.16e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.82e+00 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 13649 2.61 - 5.22: 322 5.22 - 7.84: 19 7.84 - 10.45: 5 10.45 - 13.06: 3 Bond angle restraints: 13998 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C8 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 118.25 105.19 13.06 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 117.19 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CA GLU A 144 " pdb=" CB GLU A 144 " pdb=" CG GLU A 144 " ideal model delta sigma weight residual 114.10 106.39 7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 100.07 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.37 117.87 -4.50 1.34e+00 5.57e-01 1.13e+01 ... (remaining 13993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6129 35.92 - 71.84: 100 71.84 - 107.76: 26 107.76 - 143.69: 4 143.69 - 179.61: 13 Dihedral angle restraints: 6272 sinusoidal: 2598 harmonic: 3674 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.78 148.22 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" CA GLY A 563 " pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 61 " pdb=" C LYS C 61 " pdb=" N ARG C 62 " pdb=" CA ARG C 62 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1236 0.078 - 0.156: 263 0.156 - 0.233: 23 0.233 - 0.311: 1 0.311 - 0.389: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.59 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1522 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.44e-02 2.64e+01 pdb=" NE ARG C 147 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.108 9.50e-02 1.11e+02 6.22e-02 2.04e+01 pdb=" NE ARG A 278 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1749 2.76 - 3.30: 9944 3.30 - 3.83: 16237 3.83 - 4.37: 19160 4.37 - 4.90: 33637 Nonbonded interactions: 80727 Sorted by model distance: nonbonded pdb=" OD2 ASP A 507 " pdb=" OG SER C 350 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.288 3.120 nonbonded pdb=" NZ LYS A 246 " pdb=" OE1 GLN A 639 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU A 511 " pdb=" N THR C 351 " model vdw 2.300 3.120 ... (remaining 80722 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.010 0.066 10365 Z= 0.408 Angle : 0.981 13.060 13998 Z= 0.567 Chirality : 0.063 0.389 1525 Planarity : 0.008 0.108 1792 Dihedral : 17.984 179.608 3904 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.20), residues: 1237 helix: -0.99 (0.17), residues: 605 sheet: -0.26 (0.37), residues: 161 loop : -0.14 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.010 ARG C 147 TYR 0.036 0.007 TYR A 439 PHE 0.031 0.003 PHE A 586 TRP 0.027 0.004 TRP C 86 HIS 0.014 0.003 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.41 (10365) covalent geometry : angle 0.98058 / 0.57 (13998) hydrogen bonds : bond 0.15701 / 10.04 ( 527) hydrogen bonds : angle 6.82009 / 4.66 ( 1491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 ASP cc_start: 0.7468 (t70) cc_final: 0.6992 (t0) REVERT: C 43 VAL cc_start: 0.9134 (t) cc_final: 0.8692 (p) REVERT: B 32 CYS cc_start: 0.6356 (m) cc_final: 0.5939 (m) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1184 time to fit residues: 23.5771 Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN A 264 GLN A 354 HIS A 398 ASN A 406 HIS A 410 ASN A 497 ASN A 638 HIS A 657 HIS C 137 GLN B 75 GLN B 147 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.068155 restraints weight = 21083.219| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.13 r_work: 0.2880 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10365 Z= 0.157 Angle : 0.639 7.936 13998 Z= 0.332 Chirality : 0.044 0.373 1525 Planarity : 0.004 0.058 1792 Dihedral : 17.848 168.346 1426 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.92 % Allowed : 5.45 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.23), residues: 1237 helix: 1.18 (0.20), residues: 627 sheet: 0.52 (0.42), residues: 153 loop : 0.44 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 41 TYR 0.018 0.002 TYR A 758 PHE 0.018 0.001 PHE C 255 TRP 0.014 0.002 TRP A 484 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10365) covalent geometry : angle 0.63876 / 0.33 (13998) hydrogen bonds : bond 0.04470 / 2.83 ( 527) hydrogen bonds : angle 4.67463 / 3.17 ( 1491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8742 (m-80) cc_final: 0.8447 (m-80) REVERT: A 177 MET cc_start: 0.8682 (mtt) cc_final: 0.8435 (mtt) REVERT: A 503 MET cc_start: 0.8437 (mtm) cc_final: 0.8232 (mtm) REVERT: A 507 ASP cc_start: 0.8479 (t70) cc_final: 0.7576 (t0) REVERT: A 555 ASP cc_start: 0.8005 (t0) cc_final: 0.7726 (t0) REVERT: C 123 MET cc_start: 0.8957 (mmm) cc_final: 0.8248 (mmm) REVERT: C 157 ASP cc_start: 0.8056 (m-30) cc_final: 0.7683 (m-30) REVERT: C 205 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: B 36 MET cc_start: 0.8913 (mtt) cc_final: 0.8620 (mmm) REVERT: B 105 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7430 (tpp) outliers start: 10 outliers final: 4 residues processed: 115 average time/residue: 0.0761 time to fit residues: 13.7697 Evaluate side-chains 84 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 140 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 26 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066758 restraints weight = 21348.819| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.17 r_work: 0.2843 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10365 Z= 0.183 Angle : 0.592 7.520 13998 Z= 0.305 Chirality : 0.044 0.319 1525 Planarity : 0.004 0.045 1792 Dihedral : 16.924 168.941 1426 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.39 % Allowed : 6.65 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1237 helix: 1.79 (0.21), residues: 612 sheet: 0.74 (0.40), residues: 159 loop : 0.59 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 177 TYR 0.014 0.001 TYR A 259 PHE 0.017 0.001 PHE C 255 TRP 0.014 0.001 TRP C 340 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (10365) covalent geometry : angle 0.59167 / 0.31 (13998) hydrogen bonds : bond 0.04244 / 2.71 ( 527) hydrogen bonds : angle 4.38172 / 2.96 ( 1491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8750 (m-80) cc_final: 0.8457 (m-80) REVERT: A 305 MET cc_start: 0.8868 (tpp) cc_final: 0.8271 (tpp) REVERT: A 503 MET cc_start: 0.8496 (mtm) cc_final: 0.8049 (mmm) REVERT: A 507 ASP cc_start: 0.8562 (t70) cc_final: 0.7605 (t0) REVERT: A 556 LYS cc_start: 0.8734 (mttt) cc_final: 0.8449 (mttm) REVERT: C 14 SER cc_start: 0.8523 (p) cc_final: 0.8106 (p) REVERT: C 157 ASP cc_start: 0.8038 (m-30) cc_final: 0.7534 (m-30) REVERT: C 205 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: B 93 PHE cc_start: 0.8437 (m-80) cc_final: 0.7912 (m-80) REVERT: B 105 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7490 (tpp) outliers start: 15 outliers final: 4 residues processed: 93 average time/residue: 0.0781 time to fit residues: 11.2224 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN C 371 HIS 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 = 0.100718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.068222 restraints weight = 21390.790| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.20 r_work: 0.2876 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10365 Z= 0.128 Angle : 0.548 8.851 13998 Z= 0.275 Chirality : 0.042 0.370 1525 Planarity : 0.004 0.042 1792 Dihedral : 15.681 170.280 1426 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.02 % Allowed : 7.58 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1237 helix: 2.03 (0.21), residues: 619 sheet: 0.69 (0.39), residues: 161 loop : 0.73 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 779 TYR 0.011 0.001 TYR A 758 PHE 0.015 0.001 PHE A 553 TRP 0.014 0.001 TRP C 79 HIS 0.010 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10365) covalent geometry : angle 0.54802 / 0.27 (13998) hydrogen bonds : bond 0.03594 / 2.29 ( 527) hydrogen bonds : angle 4.12098 / 2.78 ( 1491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8759 (m-80) cc_final: 0.8420 (m-80) REVERT: A 364 MET cc_start: 0.9151 (mmt) cc_final: 0.8744 (mmt) REVERT: A 503 MET cc_start: 0.8411 (mtm) cc_final: 0.8026 (mmm) REVERT: A 507 ASP cc_start: 0.8514 (t70) cc_final: 0.7506 (t0) REVERT: A 575 GLU cc_start: 0.8445 (mp0) cc_final: 0.8138 (mm-30) REVERT: C 14 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 123 MET cc_start: 0.8918 (mmm) cc_final: 0.8388 (mmm) REVERT: C 157 ASP cc_start: 0.7994 (m-30) cc_final: 0.7430 (m-30) REVERT: C 167 GLU cc_start: 0.8487 (mp0) cc_final: 0.8284 (mp0) REVERT: C 205 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 36 MET cc_start: 0.8954 (mtt) cc_final: 0.8579 (mtt) REVERT: B 73 MET cc_start: 0.5858 (mmm) cc_final: 0.4899 (ptt) REVERT: B 93 PHE cc_start: 0.8379 (m-80) cc_final: 0.7913 (m-80) REVERT: B 105 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7230 (tpp) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.0762 time to fit residues: 11.3579 Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.099729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.067096 restraints weight = 21501.888| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.20 r_work: 0.2855 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10365 Z= 0.154 Angle : 0.543 8.789 13998 Z= 0.273 Chirality : 0.042 0.343 1525 Planarity : 0.004 0.040 1792 Dihedral : 15.526 170.797 1426 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.39 % Allowed : 8.04 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1237 helix: 2.12 (0.21), residues: 615 sheet: 0.69 (0.40), residues: 161 loop : 0.69 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.013 0.001 TYR A 259 PHE 0.024 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.012 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (10365) covalent geometry : angle 0.54275 / 0.27 (13998) hydrogen bonds : bond 0.03727 / 2.38 ( 527) hydrogen bonds : angle 4.06878 / 2.75 ( 1491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8739 (m-80) cc_final: 0.8392 (m-80) REVERT: A 39 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: A 132 MET cc_start: 0.7764 (ttm) cc_final: 0.7053 (tpp) REVERT: A 197 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 305 MET cc_start: 0.8754 (tpp) cc_final: 0.8181 (tpp) REVERT: A 364 MET cc_start: 0.9107 (mmt) cc_final: 0.8682 (mmt) REVERT: A 503 MET cc_start: 0.8475 (mtm) cc_final: 0.8093 (mmm) REVERT: A 507 ASP cc_start: 0.8546 (t70) cc_final: 0.7526 (t0) REVERT: A 575 GLU cc_start: 0.8546 (mp0) cc_final: 0.8332 (mm-30) REVERT: C 14 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8278 (p) REVERT: C 167 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: C 205 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: B 93 PHE cc_start: 0.8378 (m-80) cc_final: 0.7908 (m-80) REVERT: B 105 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7228 (tpp) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.0743 time to fit residues: 10.1922 Evaluate side-chains 89 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067317 restraints weight = 21641.593| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.21 r_work: 0.2852 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10365 Z= 0.145 Angle : 0.538 7.937 13998 Z= 0.268 Chirality : 0.042 0.332 1525 Planarity : 0.004 0.042 1792 Dihedral : 15.626 172.993 1426 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.85 % Allowed : 8.69 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1237 helix: 2.09 (0.21), residues: 621 sheet: 0.62 (0.40), residues: 162 loop : 0.62 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.012 0.001 TYR A 259 PHE 0.020 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.010 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10365) covalent geometry : angle 0.53826 / 0.27 (13998) hydrogen bonds : bond 0.03639 / 2.31 ( 527) hydrogen bonds : angle 4.01874 / 2.72 ( 1491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8740 (m-80) cc_final: 0.8377 (m-80) REVERT: A 39 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: A 132 MET cc_start: 0.7856 (ttm) cc_final: 0.7225 (tpp) REVERT: A 197 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 364 MET cc_start: 0.9077 (mmt) cc_final: 0.8677 (mmt) REVERT: A 503 MET cc_start: 0.8496 (mtm) cc_final: 0.8131 (mmm) REVERT: A 507 ASP cc_start: 0.8612 (t70) cc_final: 0.7600 (t0) REVERT: A 555 ASP cc_start: 0.8110 (t0) cc_final: 0.7888 (t0) REVERT: C 14 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (p) REVERT: C 157 ASP cc_start: 0.7971 (m-30) cc_final: 0.7376 (m-30) REVERT: C 167 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: C 176 MET cc_start: 0.9176 (mmm) cc_final: 0.8914 (tpp) REVERT: C 205 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8094 (pm20) REVERT: C 316 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: B 73 MET cc_start: 0.5882 (mmm) cc_final: 0.4977 (ptt) REVERT: B 93 PHE cc_start: 0.8386 (m-80) cc_final: 0.7933 (m-80) REVERT: B 105 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7275 (tpp) REVERT: B 119 LYS cc_start: 0.8406 (mmtm) cc_final: 0.7745 (tppt) outliers start: 20 outliers final: 9 residues processed: 93 average time/residue: 0.0719 time to fit residues: 10.5747 Evaluate side-chains 93 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 7 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067919 restraints weight = 21289.190| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.19 r_work: 0.2869 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10365 Z= 0.125 Angle : 0.518 7.685 13998 Z= 0.258 Chirality : 0.041 0.319 1525 Planarity : 0.003 0.039 1792 Dihedral : 15.851 176.763 1426 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.57 % Allowed : 10.07 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.24), residues: 1237 helix: 2.19 (0.21), residues: 614 sheet: 0.57 (0.40), residues: 162 loop : 0.58 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.010 0.001 TYR A 259 PHE 0.018 0.001 PHE A 553 TRP 0.013 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (10365) covalent geometry : angle 0.51786 / 0.26 (13998) hydrogen bonds : bond 0.03444 / 2.20 ( 527) hydrogen bonds : angle 3.93278 / 2.66 ( 1491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8736 (m-80) cc_final: 0.8360 (m-80) REVERT: A 39 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7855 (pm20) REVERT: A 132 MET cc_start: 0.7877 (ttm) cc_final: 0.7226 (tpp) REVERT: A 305 MET cc_start: 0.8773 (tpp) cc_final: 0.8263 (tpp) REVERT: A 364 MET cc_start: 0.9070 (mmt) cc_final: 0.8716 (mpp) REVERT: A 503 MET cc_start: 0.8453 (mtm) cc_final: 0.8107 (mmm) REVERT: A 507 ASP cc_start: 0.8582 (t70) cc_final: 0.7571 (t0) REVERT: A 553 PHE cc_start: 0.8184 (t80) cc_final: 0.7818 (t80) REVERT: A 555 ASP cc_start: 0.8153 (t0) cc_final: 0.7837 (t0) REVERT: C 123 MET cc_start: 0.8911 (mmm) cc_final: 0.8452 (mmm) REVERT: C 167 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: C 205 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: C 316 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: B 73 MET cc_start: 0.5728 (mmm) cc_final: 0.4706 (ptt) REVERT: B 93 PHE cc_start: 0.8385 (m-80) cc_final: 0.7997 (m-80) REVERT: B 105 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7153 (tpp) REVERT: B 119 LYS cc_start: 0.8305 (mmtm) cc_final: 0.7718 (tppt) outliers start: 17 outliers final: 9 residues processed: 96 average time/residue: 0.0802 time to fit residues: 11.9535 Evaluate side-chains 93 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.067411 restraints weight = 21265.721| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.19 r_work: 0.2854 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10365 Z= 0.143 Angle : 0.538 8.190 13998 Z= 0.267 Chirality : 0.041 0.316 1525 Planarity : 0.003 0.038 1792 Dihedral : 16.016 179.256 1426 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.66 % Allowed : 10.44 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1237 helix: 2.22 (0.21), residues: 614 sheet: 0.50 (0.39), residues: 162 loop : 0.54 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.012 0.001 TYR A 259 PHE 0.017 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.007 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10365) covalent geometry : angle 0.53838 / 0.27 (13998) hydrogen bonds : bond 0.03537 / 2.25 ( 527) hydrogen bonds : angle 3.92349 / 2.65 ( 1491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8737 (m-80) cc_final: 0.8353 (m-80) REVERT: A 39 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7847 (pm20) REVERT: A 62 LEU cc_start: 0.8822 (tp) cc_final: 0.8543 (tp) REVERT: A 132 MET cc_start: 0.7939 (ttm) cc_final: 0.7368 (tpp) REVERT: A 305 MET cc_start: 0.8787 (tpp) cc_final: 0.8164 (tpp) REVERT: A 364 MET cc_start: 0.9073 (mmt) cc_final: 0.8713 (mpp) REVERT: A 503 MET cc_start: 0.8504 (mtm) cc_final: 0.8161 (mmm) REVERT: A 507 ASP cc_start: 0.8617 (t70) cc_final: 0.7587 (t0) REVERT: A 555 ASP cc_start: 0.8186 (t0) cc_final: 0.7864 (t0) REVERT: C 167 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (mp0) REVERT: C 176 MET cc_start: 0.9118 (mmm) cc_final: 0.8852 (tpp) REVERT: C 205 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: C 316 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: B 73 MET cc_start: 0.5531 (mmm) cc_final: 0.4628 (ptt) REVERT: B 93 PHE cc_start: 0.8367 (m-80) cc_final: 0.7890 (m-80) REVERT: B 105 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7196 (tpp) REVERT: B 119 LYS cc_start: 0.8347 (mmtm) cc_final: 0.7752 (tppt) outliers start: 18 outliers final: 9 residues processed: 96 average time/residue: 0.0838 time to fit residues: 12.3519 Evaluate side-chains 91 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.099870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067320 restraints weight = 21319.404| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.19 r_work: 0.2855 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10365 Z= 0.142 Angle : 0.554 8.700 13998 Z= 0.272 Chirality : 0.041 0.305 1525 Planarity : 0.003 0.038 1792 Dihedral : 16.146 178.470 1426 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.24), residues: 1237 helix: 2.20 (0.21), residues: 614 sheet: 0.44 (0.40), residues: 162 loop : 0.57 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.011 0.001 TYR A 259 PHE 0.030 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.007 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10365) covalent geometry : angle 0.55407 / 0.27 (13998) hydrogen bonds : bond 0.03542 / 2.24 ( 527) hydrogen bonds : angle 3.93401 / 2.66 ( 1491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8729 (m-80) cc_final: 0.8343 (m-80) REVERT: A 39 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: A 62 LEU cc_start: 0.8813 (tp) cc_final: 0.8528 (tp) REVERT: A 132 MET cc_start: 0.7921 (ttm) cc_final: 0.7353 (tpp) REVERT: A 305 MET cc_start: 0.8829 (tpp) cc_final: 0.8138 (tpp) REVERT: A 503 MET cc_start: 0.8487 (mtm) cc_final: 0.8167 (mmm) REVERT: A 507 ASP cc_start: 0.8627 (t70) cc_final: 0.7572 (t0) REVERT: C 123 MET cc_start: 0.8909 (mmm) cc_final: 0.8446 (mmm) REVERT: C 167 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: C 205 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: C 316 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: B 73 MET cc_start: 0.5838 (mmm) cc_final: 0.5012 (ptt) REVERT: B 105 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7170 (tpp) REVERT: B 119 LYS cc_start: 0.8446 (mmtm) cc_final: 0.7830 (tppt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.0825 time to fit residues: 11.9868 Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.100085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067526 restraints weight = 21310.643| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.19 r_work: 0.2856 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10365 Z= 0.140 Angle : 0.574 15.494 13998 Z= 0.279 Chirality : 0.041 0.296 1525 Planarity : 0.003 0.037 1792 Dihedral : 16.185 179.264 1426 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 11.37 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.24), residues: 1237 helix: 2.20 (0.21), residues: 614 sheet: 0.44 (0.40), residues: 162 loop : 0.56 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 213 TYR 0.011 0.001 TYR A 259 PHE 0.029 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.014 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10365) covalent geometry : angle 0.57421 / 0.28 (13998) hydrogen bonds : bond 0.03493 / 2.21 ( 527) hydrogen bonds : angle 3.96893 / 2.71 ( 1491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.8739 (m-80) cc_final: 0.8351 (m-80) REVERT: A 62 LEU cc_start: 0.8791 (tp) cc_final: 0.8509 (tp) REVERT: A 132 MET cc_start: 0.7962 (ttm) cc_final: 0.7374 (tpp) REVERT: A 305 MET cc_start: 0.8843 (tpp) cc_final: 0.8154 (tpp) REVERT: A 503 MET cc_start: 0.8481 (mtm) cc_final: 0.8168 (mmm) REVERT: A 507 ASP cc_start: 0.8508 (t70) cc_final: 0.7498 (t0) REVERT: C 123 MET cc_start: 0.8910 (mmm) cc_final: 0.8449 (mmm) REVERT: C 167 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: C 205 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: C 316 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: C 325 MET cc_start: 0.8795 (mmm) cc_final: 0.8411 (mmt) REVERT: B 73 MET cc_start: 0.5865 (mmm) cc_final: 0.5093 (ptt) REVERT: B 105 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7248 (tpp) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.0762 time to fit residues: 10.4433 Evaluate side-chains 86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain B residue 105 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.100091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.067479 restraints weight = 21332.770| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.20 r_work: 0.2862 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10365 Z= 0.139 Angle : 0.580 15.801 13998 Z= 0.283 Chirality : 0.041 0.290 1525 Planarity : 0.003 0.037 1792 Dihedral : 16.203 179.407 1426 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.02 % Allowed : 11.46 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.24), residues: 1237 helix: 2.20 (0.22), residues: 614 sheet: 0.39 (0.40), residues: 162 loop : 0.54 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.011 0.001 TYR A 259 PHE 0.029 0.001 PHE B 67 TRP 0.014 0.001 TRP C 79 HIS 0.013 0.001 HIS B 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10365) covalent geometry : angle 0.58010 / 0.28 (13998) hydrogen bonds : bond 0.03532 / 2.26 ( 527) hydrogen bonds : angle 3.98012 / 2.73 ( 1491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.18 seconds wall clock time: 44 minutes 24.40 seconds (2664.40 seconds total)