Starting phenix.real_space_refine on Fri Oct 23 11:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nv0_12601/10_2026/7nv0_12601.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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 55 5.49 5 S 66 5.16 5 C 6093 2.51 5 N 1701 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9928 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3162 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 15, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 6, 'PHE:plan': 5, 'GLU:plan': 13, 'ASN:plan1': 2, 'ASP:plan': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1864 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1902 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1888 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Unusual residues: {'DOC': 1} Classifications: {'DNA': 24, 'undetermined': 1} Link IDs: {'rna3p': 23, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 571 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.25 Number of scatterers: 9928 At special positions: 0 Unit cell: (121.632, 109.686, 115.116, 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 66 16.00 P 55 15.00 O 2013 8.00 N 1701 7.00 C 6093 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 243.6 milliseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 26.4% alpha, 25.8% beta 24 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.676A pdb=" N GLN A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'A' and resid 110 through 118 removed outlier: 4.036A pdb=" N GLU A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 4.532A pdb=" N ARG A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 189 removed outlier: 3.799A pdb=" N LYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.523A pdb=" N GLN A 212 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.925A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.647A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.542A pdb=" N LYS A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.542A pdb=" N LEU A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.609A pdb=" N LEU A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 400 removed outlier: 3.858A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 removed outlier: 4.029A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 5.235A pdb=" N GLU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 removed outlier: 4.056A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 removed outlier: 4.526A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'C' and resid 11 through 16 removed outlier: 3.532A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.107A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.694A pdb=" N ALA C 218 " --> pdb=" O PHE C 215 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR C 219 " --> pdb=" O THR C 216 " (cutoff:3.500A) Proline residue: C 220 - end of helix Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 72 through 79 Processing helix chain 'D' and resid 141 through 149 Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.557A pdb=" N LEU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.227A pdb=" N ALA A 129 " --> pdb=" O VAL A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 415 through 421 removed outlier: 6.660A pdb=" N LYS A 461 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET A 509 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LYS A 459 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 511 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR A 457 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE A 513 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 455 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR A 455 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N SER A 476 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N THR A 457 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 11.872A pdb=" N VAL A 474 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N LYS A 459 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N SER A 472 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 10.963A pdb=" N LYS A 461 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 11.835A pdb=" N ARG A 470 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.676A pdb=" N VAL B 111 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 71 removed outlier: 6.900A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AA8, first strand: chain 'C' and resid 26 through 30 Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.347A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 59 through 61 Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 71 removed outlier: 7.458A pdb=" N GLU D 25 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET D 40 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 0.96 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: 2259 1.33 - 1.45: 2177 1.45 - 1.57: 5527 1.57 - 1.69: 107 1.69 - 1.81: 109 Bond restraints: 10179 Sorted by residual: bond pdb=" O3B TTP A 901 " pdb=" PG TTP A 901 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" P DOC P 25 " pdb=" O5' DOC P 25 " ideal model delta sigma weight residual 1.730 1.593 0.137 2.00e-02 2.50e+03 4.66e+01 bond pdb=" C3' DA P 17 " pdb=" O3' DA P 17 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.19e+01 bond pdb=" C3' DA T 3 " pdb=" O3' DA T 3 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C3' DG P 19 " pdb=" O3' DG P 19 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 1.98e+01 ... (remaining 10174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 13493 2.64 - 5.28: 449 5.28 - 7.93: 40 7.93 - 10.57: 15 10.57 - 13.21: 2 Bond angle restraints: 13999 Sorted by residual: angle pdb=" O4' DT P 6 " pdb=" C1' DT P 6 " pdb=" N1 DT P 6 " ideal model delta sigma weight residual 108.00 111.28 -3.28 7.00e-01 2.04e+00 2.20e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O5' DA T 22 " pdb=" C5' DA T 22 " pdb=" C4' DA T 22 " ideal model delta sigma weight residual 109.40 113.08 -3.68 8.00e-01 1.56e+00 2.12e+01 angle pdb=" O4' DT P 23 " pdb=" C1' DT P 23 " pdb=" N1 DT P 23 " ideal model delta sigma weight residual 108.00 111.20 -3.20 7.00e-01 2.04e+00 2.09e+01 angle pdb=" O5' DA P 20 " pdb=" C5' DA P 20 " pdb=" C4' DA P 20 " ideal model delta sigma weight residual 109.40 112.99 -3.59 8.00e-01 1.56e+00 2.02e+01 ... (remaining 13994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5008 17.43 - 34.86: 744 34.86 - 52.29: 293 52.29 - 69.71: 81 69.71 - 87.14: 7 Dihedral angle restraints: 6133 sinusoidal: 2682 harmonic: 3451 Sorted by residual: dihedral pdb=" CA ASN A 464 " pdb=" C ASN A 464 " pdb=" N PHE A 465 " pdb=" CA PHE A 465 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN A 327 " pdb=" C ASN A 327 " pdb=" N LYS A 328 " pdb=" CA LYS A 328 " ideal model delta harmonic sigma weight residual -180.00 -155.07 -24.93 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP A 499 " pdb=" C ASP A 499 " pdb=" N PHE A 500 " pdb=" CA PHE A 500 " ideal model delta harmonic sigma weight residual -180.00 -155.18 -24.82 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1131 0.058 - 0.116: 414 0.116 - 0.174: 96 0.174 - 0.232: 10 0.232 - 0.290: 5 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR C 219 " pdb=" N THR C 219 " pdb=" C THR C 219 " pdb=" CB THR C 219 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CB ILE A 166 " pdb=" CA ILE A 166 " pdb=" CG1 ILE A 166 " pdb=" CG2 ILE A 166 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS A 328 " pdb=" N LYS A 328 " pdb=" C LYS A 328 " pdb=" CB LYS A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1653 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG P 24 " -0.033 2.00e-02 2.50e+03 1.82e-02 9.93e+00 pdb=" N9 DG P 24 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG P 24 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG P 24 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG P 24 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG P 24 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG P 24 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG P 24 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG P 24 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG P 24 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG P 24 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG P 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 23 " 0.032 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" N1 DT P 23 " -0.042 2.00e-02 2.50e+03 pdb=" C2 DT P 23 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT P 23 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DT P 23 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 23 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT P 23 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT P 23 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 23 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT P 23 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 139 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO C 140 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 140 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 140 " -0.036 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1280 2.74 - 3.28: 8510 3.28 - 3.82: 16418 3.82 - 4.36: 18442 4.36 - 4.90: 32043 Nonbonded interactions: 76693 Sorted by model distance: nonbonded pdb=" O LEU C 16 " pdb=" OG SER C 76 " model vdw 2.205 3.040 nonbonded pdb=" OG SER D 222 " pdb=" O LYS D 240 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 10 " pdb=" O ASN C 84 " model vdw 2.246 3.040 nonbonded pdb=" OG SER B 222 " pdb=" O THR B 224 " model vdw 2.272 3.040 nonbonded pdb=" OG SER C 134 " pdb=" O MET C 229 " model vdw 2.309 3.040 ... (remaining 76688 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 121 or (resid 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 129 or (resid 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or re \ sid 166 through 173 or (resid 174 and (name N or name CA or name C or name O or \ name CB )) or resid 175 through 255)) selection = (chain 'C' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 106 or resid 109 through 124 or (resid 125 through 126 and (name N or name CA \ or name C or name O or name CB )) or resid 127 or (resid 128 and (name N or name \ CA or name C or name O or name CB )) or resid 129 through 173 or (resid 174 and \ (name N or name CA or name C or name O or name CB )) or resid 175 through 185 o \ r resid 191 through 209 or (resid 210 and (name N or name CA or name C or name O \ or name CB )) or resid 211 through 255)) selection = (chain 'D' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 63 or (resid 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 94 or (resid 95 throug \ h 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 124 or (resid 125 through 126 and (name N or name CA or name C or name O or na \ me CB )) or resid 127 or (resid 128 and (name N or name CA or name C or name O o \ r name CB )) or resid 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 164 or (resid 165 and (name N or name CA o \ r name C or name O or name CB )) or resid 166 through 185 or resid 191 through 2 \ 09 or (resid 210 and (name N or name CA or name C or name O or name CB )) or res \ id 211 through 254 or (resid 255 and (name N or name CA or name C or name O or n \ ame CB )))) } 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: 0.150 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.830 Find NCS groups from input model: 0.130 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 0.138 10180 Z= 0.551 Angle : 1.155 13.208 13999 Z= 0.694 Chirality : 0.062 0.290 1656 Planarity : 0.006 0.065 1599 Dihedral : 19.567 87.143 3883 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 1.30 % Allowed : 13.45 % Favored : 85.25 % 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: -4.56 (0.19), residues: 1158 helix: -3.60 (0.19), residues: 289 sheet: -2.05 (0.23), residues: 386 loop : -3.34 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 97 TYR 0.028 0.004 TYR C 249 PHE 0.031 0.003 PHE B 169 TRP 0.021 0.003 TRP A 392 HIS 0.006 0.002 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.55 (10179) covalent geometry : angle 1.15550 / 0.69 (13999) hydrogen bonds : bond 0.13064 / 8.87 ( 469) hydrogen bonds : angle 6.88989 / 4.93 ( 1236) Misc. bond : bond 0.04207 / 2.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 300 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6912 (mt) cc_final: 0.6650 (mt) REVERT: A 58 LYS cc_start: 0.7220 (mtpt) cc_final: 0.6814 (mttp) REVERT: A 362 GLU cc_start: 0.7033 (tt0) cc_final: 0.6692 (tt0) REVERT: A 527 ARG cc_start: 0.7148 (ttt180) cc_final: 0.6623 (ttm110) REVERT: B 37 LEU cc_start: 0.7841 (tt) cc_final: 0.7550 (tp) REVERT: B 175 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.3159 (mt) REVERT: B 184 GLN cc_start: 0.5778 (tt0) cc_final: 0.5111 (tp-100) REVERT: B 199 MET cc_start: 0.6687 (tmm) cc_final: 0.6390 (tmm) REVERT: C 118 LEU cc_start: 0.7329 (mt) cc_final: 0.6959 (mm) REVERT: D 138 LYS cc_start: 0.7837 (tmmt) cc_final: 0.7176 (tttp) outliers start: 12 outliers final: 6 residues processed: 310 average time/residue: 0.1087 time to fit residues: 45.6924 Evaluate side-chains 245 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 238 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 291 GLN A 332 GLN A 447 GLN A 526 GLN B 65 ASN B 200 ASN C 65 ASN C 71 ASN C 84 ASN C 204 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152138 restraints weight = 12363.368| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.05 r_work: 0.3620 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10180 Z= 0.161 Angle : 0.711 8.548 13999 Z= 0.383 Chirality : 0.047 0.223 1656 Planarity : 0.004 0.049 1599 Dihedral : 20.467 80.928 1891 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.36 % Allowed : 16.81 % Favored : 79.83 % 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: -3.56 (0.21), residues: 1158 helix: -2.45 (0.25), residues: 293 sheet: -1.47 (0.24), residues: 387 loop : -2.97 (0.23), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 144 TYR 0.010 0.001 TYR C 60 PHE 0.013 0.002 PHE A 345 TRP 0.016 0.002 TRP A 392 HIS 0.004 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (10179) covalent geometry : angle 0.71126 / 0.38 (13999) hydrogen bonds : bond 0.04789 / 3.30 ( 469) hydrogen bonds : angle 5.68505 / 4.03 ( 1236) Misc. bond : bond 0.00217 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7490 (mttp) REVERT: A 398 ILE cc_start: 0.4448 (tt) cc_final: 0.4238 (tt) REVERT: A 527 ARG cc_start: 0.7145 (ttt180) cc_final: 0.6603 (ttm110) REVERT: B 40 MET cc_start: 0.7609 (ttm) cc_final: 0.7240 (mmm) REVERT: B 150 ASP cc_start: 0.7156 (p0) cc_final: 0.6919 (p0) REVERT: B 184 GLN cc_start: 0.5954 (tt0) cc_final: 0.5208 (tp-100) REVERT: B 224 THR cc_start: 0.7376 (t) cc_final: 0.7109 (p) REVERT: C 14 LYS cc_start: 0.7488 (mtpt) cc_final: 0.6666 (mttp) REVERT: C 118 LEU cc_start: 0.7395 (mt) cc_final: 0.7085 (mm) REVERT: D 64 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.6951 (mtm110) REVERT: D 138 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7154 (ttmm) outliers start: 31 outliers final: 21 residues processed: 268 average time/residue: 0.0945 time to fit residues: 35.5905 Evaluate side-chains 249 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 179 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [80, 44, 16, 100, 106, 73, 66, 23, 74, 82, 71] chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 chunk 71 optimal weight: 9.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN C 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.191444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153464 restraints weight = 12364.645| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.02 r_work: 0.3632 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10180 Z= 0.133 Angle : 0.639 10.824 13999 Z= 0.344 Chirality : 0.045 0.217 1656 Planarity : 0.004 0.042 1599 Dihedral : 20.131 84.733 1890 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.23 % Allowed : 18.55 % Favored : 77.22 % 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: -2.89 (0.22), residues: 1158 helix: -1.79 (0.26), residues: 295 sheet: -1.12 (0.25), residues: 387 loop : -2.58 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 97 TYR 0.010 0.001 TYR A 221 PHE 0.019 0.001 PHE A 299 TRP 0.016 0.002 TRP A 392 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10179) covalent geometry : angle 0.63854 / 0.34 (13999) hydrogen bonds : bond 0.04219 / 2.89 ( 469) hydrogen bonds : angle 5.25649 / 3.71 ( 1236) Misc. bond : bond 0.00143 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7454 (mttp) REVERT: A 291 GLN cc_start: 0.6334 (tp-100) cc_final: 0.6089 (tp-100) REVERT: A 295 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6752 (mtpt) REVERT: A 527 ARG cc_start: 0.7083 (ttt180) cc_final: 0.6603 (ttm110) REVERT: B 40 MET cc_start: 0.7563 (ttm) cc_final: 0.7190 (mmm) REVERT: B 70 VAL cc_start: 0.7383 (m) cc_final: 0.7110 (m) REVERT: B 150 ASP cc_start: 0.7063 (p0) cc_final: 0.6848 (p0) REVERT: B 184 GLN cc_start: 0.5937 (tt0) cc_final: 0.5227 (tp-100) REVERT: B 224 THR cc_start: 0.7285 (t) cc_final: 0.6989 (p) REVERT: B 250 TYR cc_start: 0.7539 (m-80) cc_final: 0.6987 (m-80) REVERT: C 118 LEU cc_start: 0.7371 (mt) cc_final: 0.6958 (mm) REVERT: C 146 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.6694 (mmm-85) REVERT: C 241 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6716 (mt) REVERT: D 64 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7005 (mtm110) REVERT: D 138 LYS cc_start: 0.7871 (tmmt) cc_final: 0.7208 (ttmm) outliers start: 39 outliers final: 23 residues processed: 254 average time/residue: 0.0924 time to fit residues: 33.0287 Evaluate side-chains 242 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 162 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [43, 13, 80, 3, 67, 64, 57, 104, 5, 11, 1] chunk 43 optimal weight: 0.1980 chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153786 restraints weight = 12427.926| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.10 r_work: 0.3626 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10180 Z= 0.144 Angle : 0.626 7.657 13999 Z= 0.336 Chirality : 0.045 0.196 1656 Planarity : 0.004 0.040 1599 Dihedral : 19.953 86.759 1890 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.66 % Allowed : 19.63 % Favored : 75.70 % 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: -2.38 (0.23), residues: 1158 helix: -1.26 (0.29), residues: 289 sheet: -0.83 (0.25), residues: 395 loop : -2.36 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 175 TYR 0.011 0.001 TYR A 50 PHE 0.019 0.002 PHE A 299 TRP 0.007 0.001 TRP A 392 HIS 0.002 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10179) covalent geometry : angle 0.62635 / 0.34 (13999) hydrogen bonds : bond 0.04247 / 2.90 ( 469) hydrogen bonds : angle 5.07053 / 3.58 ( 1236) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7554 (t80) cc_final: 0.7125 (t80) REVERT: A 58 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7368 (mttp) REVERT: A 118 ARG cc_start: 0.6978 (ptm160) cc_final: 0.6775 (ptm160) REVERT: A 295 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6821 (mtpt) REVERT: A 398 ILE cc_start: 0.4461 (tt) cc_final: 0.4209 (tt) REVERT: A 527 ARG cc_start: 0.7095 (ttt180) cc_final: 0.6549 (ttm110) REVERT: B 70 VAL cc_start: 0.7308 (m) cc_final: 0.7013 (m) REVERT: B 75 MET cc_start: 0.6971 (ttt) cc_final: 0.6311 (ttt) REVERT: B 184 GLN cc_start: 0.5911 (tt0) cc_final: 0.5230 (tp-100) REVERT: B 224 THR cc_start: 0.7350 (t) cc_final: 0.7099 (p) REVERT: B 244 MET cc_start: 0.7371 (tpp) cc_final: 0.7144 (mmm) REVERT: B 250 TYR cc_start: 0.7538 (m-80) cc_final: 0.7044 (m-80) REVERT: C 14 LYS cc_start: 0.7229 (mtpt) cc_final: 0.6547 (mttt) REVERT: C 146 ARG cc_start: 0.7001 (tpp-160) cc_final: 0.6716 (mmm-85) REVERT: D 64 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7017 (mtm110) REVERT: D 138 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7351 (ttmm) outliers start: 43 outliers final: 34 residues processed: 259 average time/residue: 0.0949 time to fit residues: 34.7948 Evaluate side-chains 260 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [105, 14, 99, 101, 92, 90, 102, 11, 7, 23, 91] chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.192605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154188 restraints weight = 12329.267| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.04 r_work: 0.3651 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10180 Z= 0.116 Angle : 0.596 9.583 13999 Z= 0.320 Chirality : 0.044 0.202 1656 Planarity : 0.003 0.040 1599 Dihedral : 19.823 87.700 1890 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.80 % Allowed : 21.91 % Favored : 74.30 % 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: -2.07 (0.24), residues: 1158 helix: -0.91 (0.30), residues: 291 sheet: -0.71 (0.25), residues: 400 loop : -2.17 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 300 TYR 0.008 0.001 TYR D 239 PHE 0.017 0.001 PHE A 299 TRP 0.007 0.001 TRP A 392 HIS 0.002 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (10179) covalent geometry : angle 0.59643 / 0.32 (13999) hydrogen bonds : bond 0.03838 / 2.62 ( 469) hydrogen bonds : angle 4.93706 / 3.48 ( 1236) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7537 (t80) cc_final: 0.7013 (t80) REVERT: A 58 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7352 (mttp) REVERT: A 63 ARG cc_start: 0.7446 (mtt-85) cc_final: 0.7128 (mtp85) REVERT: A 343 MET cc_start: 0.6415 (mmm) cc_final: 0.6152 (mmp) REVERT: A 398 ILE cc_start: 0.4594 (tt) cc_final: 0.4308 (tt) REVERT: A 449 GLU cc_start: 0.7871 (mp0) cc_final: 0.7604 (mp0) REVERT: A 527 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6601 (ttm110) REVERT: B 70 VAL cc_start: 0.7227 (m) cc_final: 0.6997 (m) REVERT: B 184 GLN cc_start: 0.5908 (tt0) cc_final: 0.5209 (tp-100) REVERT: B 224 THR cc_start: 0.7306 (t) cc_final: 0.7046 (p) REVERT: B 244 MET cc_start: 0.7353 (tpp) cc_final: 0.7121 (mmm) REVERT: B 250 TYR cc_start: 0.7546 (m-80) cc_final: 0.7083 (m-80) REVERT: C 14 LYS cc_start: 0.7106 (mtpt) cc_final: 0.6489 (mttt) REVERT: C 25 GLU cc_start: 0.8467 (pt0) cc_final: 0.8151 (pt0) REVERT: C 91 ARG cc_start: 0.6353 (ttm110) cc_final: 0.6011 (ttm110) REVERT: C 98 THR cc_start: 0.7482 (p) cc_final: 0.7250 (p) REVERT: C 146 ARG cc_start: 0.7099 (tpp-160) cc_final: 0.6820 (mmm-85) REVERT: C 181 LYS cc_start: 0.7863 (tptp) cc_final: 0.7323 (tppt) REVERT: D 25 GLU cc_start: 0.6736 (mp0) cc_final: 0.6415 (mp0) REVERT: D 64 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7065 (mtm110) REVERT: D 138 LYS cc_start: 0.7815 (tmmt) cc_final: 0.7152 (ttmm) outliers start: 35 outliers final: 25 residues processed: 254 average time/residue: 0.0930 time to fit residues: 33.1692 Evaluate side-chains 243 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [100, 40, 89, 76, 27, 43, 29, 24, 109, 106, 73] chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 0.0010 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN C 71 ASN D 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153549 restraints weight = 12319.382| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.05 r_work: 0.3629 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10180 Z= 0.124 Angle : 0.596 10.183 13999 Z= 0.318 Chirality : 0.044 0.192 1656 Planarity : 0.003 0.038 1599 Dihedral : 19.727 87.752 1890 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.34 % Allowed : 21.80 % Favored : 73.86 % 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: -1.90 (0.24), residues: 1158 helix: -0.80 (0.30), residues: 294 sheet: -0.56 (0.25), residues: 395 loop : -2.08 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.008 0.001 TYR D 239 PHE 0.015 0.001 PHE A 111 TRP 0.007 0.001 TRP D 28 HIS 0.002 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10179) covalent geometry : angle 0.59572 / 0.32 (13999) hydrogen bonds : bond 0.03912 / 2.68 ( 469) hydrogen bonds : angle 4.83413 / 3.41 ( 1236) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7573 (t80) cc_final: 0.7030 (t80) REVERT: A 58 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7329 (mttp) REVERT: A 63 ARG cc_start: 0.7500 (mtt-85) cc_final: 0.7089 (mtp85) REVERT: A 343 MET cc_start: 0.6365 (mmm) cc_final: 0.6078 (mmp) REVERT: A 398 ILE cc_start: 0.4668 (tt) cc_final: 0.4459 (tt) REVERT: A 527 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6633 (ttm110) REVERT: B 70 VAL cc_start: 0.7174 (m) cc_final: 0.6915 (m) REVERT: B 184 GLN cc_start: 0.5904 (tt0) cc_final: 0.5202 (tp-100) REVERT: B 224 THR cc_start: 0.7305 (t) cc_final: 0.7063 (p) REVERT: B 244 MET cc_start: 0.7373 (tpp) cc_final: 0.7143 (mmm) REVERT: B 250 TYR cc_start: 0.7508 (m-80) cc_final: 0.7117 (m-80) REVERT: C 12 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 14 LYS cc_start: 0.7137 (mtpt) cc_final: 0.6489 (mttt) REVERT: C 91 ARG cc_start: 0.6385 (ttm110) cc_final: 0.6028 (ttm110) REVERT: C 98 THR cc_start: 0.7425 (p) cc_final: 0.7205 (p) REVERT: C 146 ARG cc_start: 0.7100 (tpp-160) cc_final: 0.6809 (mmm-85) REVERT: C 181 LYS cc_start: 0.7845 (tptp) cc_final: 0.7352 (tppt) REVERT: D 64 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7069 (mtm110) REVERT: D 138 LYS cc_start: 0.7862 (tmmt) cc_final: 0.7180 (ttmm) outliers start: 40 outliers final: 34 residues processed: 246 average time/residue: 0.0888 time to fit residues: 30.9502 Evaluate side-chains 249 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [56, 112, 32, 81, 58, 22, 96, 41, 75, 83, 102] chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN B 71 ASN C 38 GLN D 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.187206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.148251 restraints weight = 12238.637| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.04 r_work: 0.3572 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10180 Z= 0.213 Angle : 0.705 11.994 13999 Z= 0.372 Chirality : 0.047 0.166 1656 Planarity : 0.004 0.036 1599 Dihedral : 19.794 85.505 1890 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.66 % Allowed : 21.91 % Favored : 73.43 % 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: -1.98 (0.24), residues: 1158 helix: -1.00 (0.29), residues: 297 sheet: -0.61 (0.25), residues: 392 loop : -2.04 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 512 TYR 0.017 0.002 TYR D 249 PHE 0.017 0.002 PHE B 207 TRP 0.014 0.002 TRP D 28 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (10179) covalent geometry : angle 0.70545 / 0.37 (13999) hydrogen bonds : bond 0.05084 / 3.43 ( 469) hydrogen bonds : angle 5.06662 / 3.56 ( 1236) Misc. bond : bond 0.00127 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7483 (t80) cc_final: 0.6994 (t80) REVERT: A 58 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7309 (mttp) REVERT: A 63 ARG cc_start: 0.7448 (mtt-85) cc_final: 0.7148 (mtp85) REVERT: A 343 MET cc_start: 0.6463 (mmm) cc_final: 0.6112 (mmp) REVERT: A 449 GLU cc_start: 0.7867 (mp0) cc_final: 0.7545 (mp0) REVERT: A 527 ARG cc_start: 0.7184 (ttt180) cc_final: 0.6623 (ttm110) REVERT: B 70 VAL cc_start: 0.7276 (m) cc_final: 0.7053 (m) REVERT: B 174 GLU cc_start: 0.6965 (pm20) cc_final: 0.6276 (pm20) REVERT: B 184 GLN cc_start: 0.6042 (tt0) cc_final: 0.5192 (tp-100) REVERT: B 224 THR cc_start: 0.7410 (t) cc_final: 0.7153 (p) REVERT: B 244 MET cc_start: 0.7369 (tpp) cc_final: 0.7159 (mmm) REVERT: B 250 TYR cc_start: 0.7456 (m-80) cc_final: 0.7097 (m-80) REVERT: C 12 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7520 (mp) REVERT: C 14 LYS cc_start: 0.7484 (mtpt) cc_final: 0.6734 (mttt) REVERT: C 91 ARG cc_start: 0.6597 (ttm110) cc_final: 0.6251 (ttm-80) REVERT: C 132 GLU cc_start: 0.7020 (pm20) cc_final: 0.6781 (pm20) REVERT: D 64 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7065 (mtm110) REVERT: D 65 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7168 (m-40) REVERT: D 138 LYS cc_start: 0.8051 (tmmt) cc_final: 0.7287 (tttp) outliers start: 43 outliers final: 36 residues processed: 241 average time/residue: 0.0865 time to fit residues: 29.6556 Evaluate side-chains 250 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [16, 23, 86, 73, 104, 80, 47, 9, 7, 102, 93] chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147476 restraints weight = 12251.511| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.13 r_work: 0.3571 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10180 Z= 0.213 Angle : 0.711 12.859 13999 Z= 0.374 Chirality : 0.047 0.171 1656 Planarity : 0.004 0.034 1599 Dihedral : 19.816 82.269 1890 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.56 % Allowed : 22.78 % Favored : 72.67 % 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 (0.23), residues: 1158 helix: -1.02 (0.29), residues: 294 sheet: -0.63 (0.25), residues: 396 loop : -2.03 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 470 TYR 0.013 0.002 TYR A 112 PHE 0.019 0.002 PHE A 49 TRP 0.017 0.002 TRP D 28 HIS 0.004 0.001 HIS A 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (10179) covalent geometry : angle 0.71099 / 0.37 (13999) hydrogen bonds : bond 0.04940 / 3.31 ( 469) hydrogen bonds : angle 5.11145 / 3.59 ( 1236) Misc. bond : bond 0.00109 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7558 (t80) cc_final: 0.7027 (t80) REVERT: A 58 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7447 (mttp) REVERT: A 63 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7047 (mtp85) REVERT: A 67 MET cc_start: 0.7043 (tpt) cc_final: 0.6450 (tpt) REVERT: A 343 MET cc_start: 0.6487 (mmm) cc_final: 0.6140 (mmp) REVERT: A 527 ARG cc_start: 0.7304 (ttt180) cc_final: 0.6593 (ttm110) REVERT: B 174 GLU cc_start: 0.7036 (pm20) cc_final: 0.6333 (pm20) REVERT: B 184 GLN cc_start: 0.6096 (tt0) cc_final: 0.5240 (tp-100) REVERT: B 224 THR cc_start: 0.7380 (t) cc_final: 0.7116 (m) REVERT: B 244 MET cc_start: 0.7314 (tpp) cc_final: 0.7084 (mmm) REVERT: B 250 TYR cc_start: 0.7488 (m-80) cc_final: 0.7031 (m-80) REVERT: C 12 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7540 (mp) REVERT: C 14 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6677 (mttt) REVERT: C 91 ARG cc_start: 0.6618 (ttm110) cc_final: 0.6138 (ttm-80) REVERT: C 132 GLU cc_start: 0.7092 (pm20) cc_final: 0.6820 (pm20) REVERT: C 146 ARG cc_start: 0.7046 (tpp-160) cc_final: 0.6569 (mmm-85) REVERT: C 205 LEU cc_start: 0.8294 (mt) cc_final: 0.8058 (mm) REVERT: D 64 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7045 (mtm110) REVERT: D 65 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7144 (m-40) REVERT: D 138 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7118 (tttp) outliers start: 42 outliers final: 36 residues processed: 239 average time/residue: 0.0908 time to fit residues: 30.8933 Evaluate side-chains 246 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [24, 41, 113, 21, 64, 9, 48, 105, 26, 96, 29] chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.0000 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.195237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155742 restraints weight = 12159.998| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.16 r_work: 0.3638 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10180 Z= 0.125 Angle : 0.632 11.955 13999 Z= 0.334 Chirality : 0.044 0.202 1656 Planarity : 0.003 0.037 1599 Dihedral : 19.678 85.715 1890 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.25 % Allowed : 24.19 % Favored : 72.56 % 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: -1.65 (0.24), residues: 1158 helix: -0.66 (0.29), residues: 303 sheet: -0.43 (0.25), residues: 398 loop : -1.90 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 210 TYR 0.009 0.001 TYR A 112 PHE 0.031 0.001 PHE A 49 TRP 0.009 0.001 TRP D 28 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10179) covalent geometry : angle 0.63212 / 0.33 (13999) hydrogen bonds : bond 0.03813 / 2.57 ( 469) hydrogen bonds : angle 4.88368 / 3.43 ( 1236) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7518 (t80) cc_final: 0.6928 (t80) REVERT: A 58 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7336 (mttp) REVERT: A 63 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.7042 (mtp85) REVERT: A 67 MET cc_start: 0.6792 (tpt) cc_final: 0.6278 (tpt) REVERT: A 343 MET cc_start: 0.6454 (mmm) cc_final: 0.6176 (mmp) REVERT: A 362 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: A 527 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6676 (ttm110) REVERT: B 70 VAL cc_start: 0.7133 (m) cc_final: 0.6781 (m) REVERT: B 168 LYS cc_start: 0.6941 (tttm) cc_final: 0.6726 (tptm) REVERT: B 184 GLN cc_start: 0.6083 (tt0) cc_final: 0.5044 (tp-100) REVERT: B 224 THR cc_start: 0.7298 (t) cc_final: 0.7055 (m) REVERT: B 250 TYR cc_start: 0.7508 (m-80) cc_final: 0.7179 (m-80) REVERT: C 12 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7672 (mp) REVERT: C 14 LYS cc_start: 0.7199 (mtpt) cc_final: 0.6345 (mmtm) REVERT: C 91 ARG cc_start: 0.6463 (ttm110) cc_final: 0.6187 (ttm-80) REVERT: C 146 ARG cc_start: 0.6958 (tpp-160) cc_final: 0.6509 (mmm-85) REVERT: C 205 LEU cc_start: 0.8230 (mt) cc_final: 0.7869 (mm) REVERT: D 64 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.6994 (mtm110) REVERT: D 138 LYS cc_start: 0.7693 (tmmt) cc_final: 0.6963 (ttmm) outliers start: 30 outliers final: 25 residues processed: 242 average time/residue: 0.0985 time to fit residues: 33.4374 Evaluate side-chains 240 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 179 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [94, 30, 78, 40, 88, 5, 43, 4, 7, 57, 86] chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 88 optimal weight: 0.1980 chunk 5 optimal weight: 0.0670 chunk 43 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155764 restraints weight = 12032.401| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.02 r_work: 0.3666 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10180 Z= 0.125 Angle : 0.626 11.742 13999 Z= 0.331 Chirality : 0.044 0.197 1656 Planarity : 0.003 0.035 1599 Dihedral : 19.622 85.161 1890 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.25 % Allowed : 24.30 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.24), residues: 1158 helix: -0.45 (0.30), residues: 297 sheet: -0.31 (0.26), residues: 396 loop : -1.83 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 53 TYR 0.009 0.001 TYR D 239 PHE 0.028 0.001 PHE A 49 TRP 0.018 0.002 TRP A 392 HIS 0.002 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10179) covalent geometry : angle 0.62568 / 0.33 (13999) hydrogen bonds : bond 0.03867 / 2.61 ( 469) hydrogen bonds : angle 4.79641 / 3.38 ( 1236) Misc. bond : bond 0.00001 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7550 (t80) cc_final: 0.7017 (t80) REVERT: A 58 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7337 (mttp) REVERT: A 63 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.7169 (mtp85) REVERT: A 67 MET cc_start: 0.6828 (tpt) cc_final: 0.6128 (tpt) REVERT: A 343 MET cc_start: 0.6346 (mmm) cc_final: 0.6096 (mmp) REVERT: A 527 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6728 (ttm110) REVERT: B 184 GLN cc_start: 0.6182 (tt0) cc_final: 0.5166 (tp-100) REVERT: B 224 THR cc_start: 0.7418 (t) cc_final: 0.7167 (m) REVERT: B 250 TYR cc_start: 0.7591 (m-80) cc_final: 0.7291 (m-80) REVERT: C 12 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7683 (mp) REVERT: C 14 LYS cc_start: 0.7215 (mtpt) cc_final: 0.6446 (mmtm) REVERT: C 91 ARG cc_start: 0.6500 (ttm110) cc_final: 0.6209 (ttm-80) REVERT: C 98 THR cc_start: 0.7459 (p) cc_final: 0.7237 (p) REVERT: C 146 ARG cc_start: 0.7189 (tpp-160) cc_final: 0.6807 (mmm-85) REVERT: C 205 LEU cc_start: 0.8224 (mt) cc_final: 0.7992 (mm) REVERT: D 64 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7086 (mtm110) REVERT: D 138 LYS cc_start: 0.7863 (tmmt) cc_final: 0.7037 (tttp) outliers start: 30 outliers final: 23 residues processed: 240 average time/residue: 0.0942 time to fit residues: 31.8121 Evaluate side-chains 230 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 153 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [89, 90, 70, 85, 91, 108, 86, 115, 54, 105, 63] chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.0010 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.190566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152623 restraints weight = 12239.758| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.10 r_work: 0.3618 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10180 Z= 0.153 Angle : 0.665 12.768 13999 Z= 0.349 Chirality : 0.045 0.198 1656 Planarity : 0.003 0.033 1599 Dihedral : 19.599 82.828 1890 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.36 % Allowed : 24.19 % Favored : 72.45 % 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: -1.54 (0.24), residues: 1158 helix: -0.57 (0.29), residues: 304 sheet: -0.33 (0.26), residues: 394 loop : -1.87 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 210 TYR 0.010 0.001 TYR A 112 PHE 0.028 0.002 PHE A 49 TRP 0.017 0.003 TRP A 392 HIS 0.003 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10179) covalent geometry : angle 0.66476 / 0.35 (13999) hydrogen bonds : bond 0.04201 / 2.82 ( 469) hydrogen bonds : angle 4.85613 / 3.42 ( 1236) Misc. bond : bond 0.00027 / 0.01 ( 1) =============================================================================== Job complete usr+sys time: 2372.70 seconds wall clock time: 41 minutes 20.11 seconds (2480.11 seconds total)