Starting phenix.real_space_refine on Fri Jul 3 10:12:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5k_29747/07_2026/8g5k_29747.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 37 5.49 5 S 78 5.16 5 C 8572 2.51 5 N 2391 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13629 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7079 Classifications: {'peptide': 905} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 60, 'TRANS': 844} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 7, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2934 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain breaks: 2 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2855 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "P" Number of atoms: 394 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Conformer: "B" Number of residues, atoms: 18, 373 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 3.10, per 1000 atoms: 0.23 Number of scatterers: 13629 At special positions: 0 Unit cell: (91.686, 101.598, 139.594, 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 78 16.00 P 37 15.00 O 2551 8.00 N 2391 7.00 C 8572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 592.3 milliseconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3046 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 34.5% alpha, 10.1% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.096A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 146 removed outlier: 3.773A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 160 Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.408A pdb=" N GLN A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 227 " --> pdb=" O CYS A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 227' Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.649A pdb=" N ASP A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.694A pdb=" N LEU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.703A pdb=" N LEU A 392 " --> pdb=" O ASN A 388 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.135A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 472 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 570 through 576 Processing helix chain 'A' and resid 793 through 809 removed outlier: 4.699A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 955 Processing helix chain 'A' and resid 958 through 968 removed outlier: 3.667A pdb=" N GLN A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 980 Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.959A pdb=" N TYR A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1093 through 1115 removed outlier: 3.921A pdb=" N VAL A1097 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1169 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.184A pdb=" N GLU B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.564A pdb=" N LEU B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.760A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.507A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 394 through 407 removed outlier: 3.881A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.618A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 100 through 120 removed outlier: 4.120A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL C 118 " --> pdb=" O TRP C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.959A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.695A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.088A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.808A pdb=" N ASP C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 215 removed outlier: 3.769A pdb=" N VAL A 213 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1132 Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.600A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA6, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.076A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.308A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.308A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 422 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4176 1.34 - 1.46: 2886 1.46 - 1.58: 6790 1.58 - 1.70: 72 1.70 - 1.82: 123 Bond restraints: 14047 Sorted by residual: bond pdb=" C3' DA P 10 " pdb=" O3' DA P 10 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.41e+01 bond pdb=" CG PRO A 241 " pdb=" CD PRO A 241 " ideal model delta sigma weight residual 1.503 1.360 0.143 3.40e-02 8.65e+02 1.77e+01 bond pdb=" C3' DT P 16 " pdb=" O3' DT P 16 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" C1' DT P 16 " pdb=" N1 DT P 16 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" C3' DA T 15 " pdb=" O3' DA T 15 " ideal model delta sigma weight residual 1.435 1.476 -0.041 1.30e-02 5.92e+03 9.97e+00 ... (remaining 14042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 19095 5.20 - 10.40: 111 10.40 - 15.60: 14 15.60 - 20.80: 2 20.80 - 26.00: 2 Bond angle restraints: 19224 Sorted by residual: angle pdb=" C3' DG P 24 " pdb=" O3' DG P 24 " pdb=" P DC P 25 " ideal model delta sigma weight residual 120.20 106.52 13.68 1.50e+00 4.44e-01 8.32e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP2 DG P 11 " ideal model delta sigma weight residual 108.00 82.00 26.00 3.00e+00 1.11e-01 7.51e+01 angle pdb=" N PRO A 241 " pdb=" CD PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 103.20 90.30 12.90 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N PRO A 241 " pdb=" CA PRO A 241 " pdb=" CB PRO A 241 " ideal model delta sigma weight residual 103.25 94.97 8.28 1.05e+00 9.07e-01 6.22e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP1 DG P 11 " ideal model delta sigma weight residual 108.00 84.73 23.27 3.00e+00 1.11e-01 6.01e+01 ... (remaining 19219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8017 35.44 - 70.88: 209 70.88 - 106.32: 12 106.32 - 141.76: 2 141.76 - 177.20: 3 Dihedral angle restraints: 8243 sinusoidal: 3527 harmonic: 4716 Sorted by residual: dihedral pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " pdb=" NH1 ARG A 309 " ideal model delta sinusoidal sigma weight residual 0.00 74.98 -74.98 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CA LEU B 106 " pdb=" C LEU B 106 " pdb=" N ARG B 107 " pdb=" CA ARG B 107 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.413: 2091 0.413 - 0.827: 5 0.827 - 1.240: 0 1.240 - 1.654: 0 1.654 - 2.067: 1 Chirality restraints: 2097 Sorted by residual: chirality pdb=" P DG P 11 " pdb=" OP1 DG P 11 " pdb=" OP2 DG P 11 " pdb=" O5' DG P 11 " both_signs ideal model delta sigma weight residual True 2.34 0.27 2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" P DG T 4 " pdb=" OP1 DG T 4 " pdb=" OP2 DG T 4 " pdb=" O5' DG T 4 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DG P 24 " pdb=" OP1 DG P 24 " pdb=" OP2 DG P 24 " pdb=" O5' DG P 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.49 2.00e-01 2.50e+01 5.98e+00 ... (remaining 2094 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 309 " -1.061 9.50e-02 1.11e+02 4.76e-01 1.36e+02 pdb=" NE ARG A 309 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 309 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 309 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 309 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 315 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO C 316 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 782 " -0.051 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO A 783 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 783 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 783 " -0.041 5.00e-02 4.00e+02 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1523 2.76 - 3.29: 13100 3.29 - 3.83: 22253 3.83 - 4.36: 25644 4.36 - 4.90: 43282 Nonbonded interactions: 105802 Sorted by model distance: nonbonded pdb=" O GLU C 113 " pdb=" OG1 THR C 116 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR A 586 " pdb=" OG SER A 590 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 457 " pdb=" O THR B 460 " model vdw 2.298 3.040 nonbonded pdb=" O PRO C 380 " pdb=" OG SER C 412 " model vdw 2.313 3.040 ... (remaining 105797 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 68 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 77 or (resid 78 and (name N or nam \ e CA or name C or name O or name CB )) or resid 79 through 83 or (resid 84 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 219 or ( \ resid 220 through 221 and (name N or name CA or name C or name O or name CB )) o \ r resid 228 through 327 or (resid 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 357 or resid 372 or (resid 3 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 374 through \ 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) or r \ esid 386 through 388 or (resid 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 428 or (resid 429 and (name N or name CA or nam \ e C or name O or name CB )) or resid 430 through 433 or (resid 434 through 435 a \ nd (name N or name CA or name C or name O or name CB )) or resid 436 through 444 \ or (resid 445 and (name N or name CA or name C or name O or name CB )) or resid \ 446 through 454 or (resid 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 485)) selection = (chain 'C' and (resid 68 through 122 or (resid 123 through 124 and (name N or na \ me CA or name C or name O or name CB )) or resid 125 or (resid 126 and (name N o \ r name CA or name C or name O or name CB )) or resid 127 through 133 or resid 17 \ 9 or (resid 180 and (name N or name CA or name C or name O or name CB )) or resi \ d 181 through 200 or (resid 201 and (name N or name CA or name C or name O or na \ me CB )) or resid 202 through 221 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 245 or (resid 246 and (name N or n \ ame CA or name C or name O or name CB )) or resid 247 through 485)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.480 Find NCS groups from input model: 0.140 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.005 0.143 14047 Z= 0.305 Angle : 1.086 25.995 19224 Z= 0.587 Chirality : 0.076 2.067 2097 Planarity : 0.012 0.476 2340 Dihedral : 15.614 177.202 5197 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer: Outliers : 0.29 % Allowed : 1.03 % Favored : 98.68 % 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: -1.76 (0.20), residues: 1611 helix: -0.02 (0.22), residues: 545 sheet: -0.32 (0.37), residues: 177 loop : -2.18 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 259 TYR 0.027 0.001 TYR C 417 PHE 0.030 0.002 PHE A 197 TRP 0.029 0.002 TRP A 607 HIS 0.011 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.31 (14047) covalent geometry : angle 1.08636 / 0.59 (19224) hydrogen bonds : bond 0.13107 / 10.11 ( 462) hydrogen bonds : angle 5.86470 / 4.75 ( 1310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.475 Fit side-chains REVERT: A 207 THR cc_start: 0.7723 (p) cc_final: 0.7482 (p) REVERT: A 416 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6380 (tp30) REVERT: A 544 MET cc_start: 0.6746 (mmm) cc_final: 0.6337 (mmm) REVERT: A 1097 VAL cc_start: 0.6574 (m) cc_final: 0.6254 (p) REVERT: A 1102 GLN cc_start: 0.7216 (mt0) cc_final: 0.6886 (mt0) REVERT: A 1156 THR cc_start: 0.7953 (m) cc_final: 0.7272 (p) REVERT: B 458 ARG cc_start: 0.8022 (ttp-170) cc_final: 0.7389 (ttp-170) REVERT: C 300 ILE cc_start: 0.8106 (mm) cc_final: 0.7787 (mt) outliers start: 4 outliers final: 0 residues processed: 266 average time/residue: 0.5241 time to fit residues: 153.8316 Evaluate side-chains 220 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 HIS A 108 GLN A 360 HIS A 404 HIS A 409 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN A 541 GLN A 550 GLN A 906 HIS A 932 HIS A 968 GLN A 970 ASN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 323 HIS B 375 HIS B 404 ASN C 133 HIS C 422 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.212260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.188961 restraints weight = 22507.129| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.41 r_work: 0.4234 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4239 r_free = 0.4239 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4239 r_free = 0.4239 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14047 Z= 0.164 Angle : 0.768 24.489 19224 Z= 0.370 Chirality : 0.065 2.071 2097 Planarity : 0.005 0.068 2340 Dihedral : 16.899 174.657 2149 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 2.57 % Allowed : 9.24 % Favored : 88.19 % 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: -1.40 (0.20), residues: 1611 helix: 0.45 (0.23), residues: 519 sheet: -0.24 (0.36), residues: 181 loop : -2.00 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 259 TYR 0.025 0.002 TYR B 206 PHE 0.023 0.002 PHE A 749 TRP 0.020 0.001 TRP A 607 HIS 0.007 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (14047) covalent geometry : angle 0.76805 / 0.37 (19224) hydrogen bonds : bond 0.04227 / 2.86 ( 462) hydrogen bonds : angle 4.74125 / 3.65 ( 1310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 100 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7213 (m) REVERT: A 220 TRP cc_start: 0.5299 (m100) cc_final: 0.4825 (m100) REVERT: A 434 TYR cc_start: 0.7634 (t80) cc_final: 0.7026 (t80) REVERT: A 465 ASP cc_start: 0.6965 (m-30) cc_final: 0.6705 (m-30) REVERT: A 544 MET cc_start: 0.6931 (mmm) cc_final: 0.6660 (mmm) REVERT: A 953 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6197 (mtm110) REVERT: A 1057 MET cc_start: 0.4130 (mmm) cc_final: 0.1970 (ptm) REVERT: A 1107 ASP cc_start: 0.6438 (m-30) cc_final: 0.6198 (m-30) REVERT: B 241 TRP cc_start: 0.7276 (t-100) cc_final: 0.7071 (t-100) REVERT: B 256 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7244 (tp) REVERT: B 404 ASN cc_start: 0.7570 (m-40) cc_final: 0.7331 (m-40) REVERT: B 458 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7753 (ttp-170) REVERT: C 300 ILE cc_start: 0.8290 (mm) cc_final: 0.8008 (mt) outliers start: 35 outliers final: 11 residues processed: 250 average time/residue: 0.5301 time to fit residues: 146.0897 Evaluate side-chains 237 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 158 optimal weight: 0.0370 chunk 75 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.209392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.186141 restraints weight = 20299.866| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 2.32 r_work: 0.4195 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4192 r_free = 0.4192 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14047 Z= 0.153 Angle : 0.725 25.294 19224 Z= 0.351 Chirality : 0.063 2.017 2097 Planarity : 0.005 0.049 2340 Dihedral : 16.857 175.049 2149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.69 % Rotamer: Outliers : 2.93 % Allowed : 12.18 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.21), residues: 1611 helix: 0.54 (0.23), residues: 525 sheet: -0.19 (0.36), residues: 183 loop : -2.00 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.024 0.001 TYR B 206 PHE 0.025 0.002 PHE A 749 TRP 0.016 0.001 TRP A 607 HIS 0.008 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (14047) covalent geometry : angle 0.72499 / 0.35 (19224) hydrogen bonds : bond 0.04102 / 2.82 ( 462) hydrogen bonds : angle 4.57299 / 3.48 ( 1310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 100 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7151 (m) REVERT: A 465 ASP cc_start: 0.6929 (m-30) cc_final: 0.6686 (m-30) REVERT: A 486 TRP cc_start: 0.7874 (p-90) cc_final: 0.7620 (p-90) REVERT: A 544 MET cc_start: 0.6928 (mmm) cc_final: 0.6631 (mmm) REVERT: A 953 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6127 (mtm110) REVERT: A 1057 MET cc_start: 0.4092 (mmm) cc_final: 0.1684 (ptm) REVERT: A 1107 ASP cc_start: 0.6544 (m-30) cc_final: 0.6335 (m-30) REVERT: B 241 TRP cc_start: 0.7356 (t-100) cc_final: 0.6931 (t-100) REVERT: B 260 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7332 (mt) REVERT: C 300 ILE cc_start: 0.8347 (mm) cc_final: 0.8038 (mt) REVERT: C 346 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6188 (mtp) REVERT: C 382 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4956 (mppt) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 0.4892 time to fit residues: 134.9020 Evaluate side-chains 249 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.207122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.183239 restraints weight = 22341.798| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.49 r_work: 0.4164 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4167 r_free = 0.4167 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14047 Z= 0.142 Angle : 0.705 25.359 19224 Z= 0.342 Chirality : 0.063 2.020 2097 Planarity : 0.005 0.047 2340 Dihedral : 16.862 174.847 2149 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.37 % Favored : 90.50 % Rotamer: Outliers : 2.79 % Allowed : 14.67 % Favored : 82.54 % 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: -1.34 (0.21), residues: 1611 helix: 0.47 (0.23), residues: 538 sheet: -0.18 (0.37), residues: 182 loop : -2.00 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 478 TYR 0.024 0.001 TYR B 206 PHE 0.022 0.002 PHE A 749 TRP 0.015 0.001 TRP A 607 HIS 0.018 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14047) covalent geometry : angle 0.70522 / 0.34 (19224) hydrogen bonds : bond 0.03794 / 2.61 ( 462) hydrogen bonds : angle 4.51232 / 3.40 ( 1310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5727 (mm110) REVERT: A 100 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7190 (m) REVERT: A 297 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6841 (mtt) REVERT: A 465 ASP cc_start: 0.6933 (m-30) cc_final: 0.6646 (m-30) REVERT: A 486 TRP cc_start: 0.7941 (p-90) cc_final: 0.7638 (p-90) REVERT: A 544 MET cc_start: 0.6920 (mmm) cc_final: 0.6610 (mmm) REVERT: A 953 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6148 (mtm110) REVERT: A 1107 ASP cc_start: 0.6544 (m-30) cc_final: 0.6330 (m-30) REVERT: B 241 TRP cc_start: 0.7372 (t-100) cc_final: 0.6959 (t-100) REVERT: B 260 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7401 (mt) REVERT: B 285 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6733 (tptp) REVERT: B 442 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7673 (tp) REVERT: C 300 ILE cc_start: 0.8302 (mm) cc_final: 0.8036 (mt) REVERT: C 346 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6235 (mtp) outliers start: 38 outliers final: 15 residues processed: 239 average time/residue: 0.4402 time to fit residues: 116.5312 Evaluate side-chains 245 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 138 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 409 ASN C 192 HIS C 467 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172804 restraints weight = 28449.871| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 2.92 r_work: 0.4011 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4015 r_free = 0.4015 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (13 function evaluations) r_final: 0.4015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14047 Z= 0.259 Angle : 0.856 25.428 19224 Z= 0.425 Chirality : 0.067 2.023 2097 Planarity : 0.006 0.065 2340 Dihedral : 17.121 174.335 2149 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.01 % Rotamer: Outliers : 3.82 % Allowed : 15.19 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.20), residues: 1611 helix: -0.28 (0.22), residues: 547 sheet: -0.50 (0.37), residues: 185 loop : -2.17 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 259 TYR 0.037 0.003 TYR B 206 PHE 0.029 0.003 PHE A 197 TRP 0.032 0.002 TRP A 607 HIS 0.016 0.002 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 (14047) covalent geometry : angle 0.85640 / 0.42 (19224) hydrogen bonds : bond 0.04968 / 3.43 ( 462) hydrogen bonds : angle 4.99880 / 3.70 ( 1310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7529 (mm) cc_final: 0.7293 (mp) REVERT: A 416 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7132 (tp30) REVERT: A 465 ASP cc_start: 0.6884 (m-30) cc_final: 0.6656 (m-30) REVERT: A 486 TRP cc_start: 0.8247 (p-90) cc_final: 0.7943 (p-90) REVERT: A 544 MET cc_start: 0.6980 (mmm) cc_final: 0.6632 (mmm) REVERT: A 898 ILE cc_start: 0.7557 (mm) cc_final: 0.7345 (mm) REVERT: A 953 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6118 (mtm110) REVERT: A 965 LEU cc_start: 0.8016 (tp) cc_final: 0.7720 (tp) REVERT: A 969 PHE cc_start: 0.7644 (m-10) cc_final: 0.7290 (m-10) REVERT: A 1072 THR cc_start: 0.6290 (m) cc_final: 0.6024 (m) REVERT: A 1111 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (mp) REVERT: B 132 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.4384 (t-170) REVERT: B 285 LYS cc_start: 0.7371 (mmmt) cc_final: 0.6864 (tptp) REVERT: B 442 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7719 (tt) REVERT: C 300 ILE cc_start: 0.8446 (mm) cc_final: 0.8214 (mt) REVERT: C 346 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6732 (mtp) REVERT: C 349 TYR cc_start: 0.5817 (m-10) cc_final: 0.5307 (m-10) REVERT: C 462 MET cc_start: 0.4678 (pp-130) cc_final: 0.4340 (pp-130) outliers start: 52 outliers final: 19 residues processed: 269 average time/residue: 0.4707 time to fit residues: 139.9858 Evaluate side-chains 263 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 79 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 277 HIS A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.200798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175529 restraints weight = 28252.980| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.88 r_work: 0.4042 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14047 Z= 0.151 Angle : 0.742 25.466 19224 Z= 0.364 Chirality : 0.063 2.015 2097 Planarity : 0.005 0.050 2340 Dihedral : 16.934 174.989 2149 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.68 % Favored : 90.19 % Rotamer: Outliers : 2.64 % Allowed : 18.42 % Favored : 78.94 % 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: -1.64 (0.20), residues: 1611 helix: 0.06 (0.22), residues: 549 sheet: -0.30 (0.39), residues: 165 loop : -2.07 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 126 TYR 0.025 0.001 TYR B 206 PHE 0.026 0.002 PHE A 749 TRP 0.020 0.002 TRP A 607 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14047) covalent geometry : angle 0.74166 / 0.36 (19224) hydrogen bonds : bond 0.04003 / 2.77 ( 462) hydrogen bonds : angle 4.70307 / 3.50 ( 1310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 416 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7080 (tp30) REVERT: A 465 ASP cc_start: 0.6836 (m-30) cc_final: 0.6561 (m-30) REVERT: A 486 TRP cc_start: 0.8178 (p-90) cc_final: 0.7880 (p-90) REVERT: A 544 MET cc_start: 0.6995 (mmm) cc_final: 0.6628 (mmm) REVERT: A 898 ILE cc_start: 0.7460 (mm) cc_final: 0.7251 (mm) REVERT: A 953 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6129 (mtm110) REVERT: A 965 LEU cc_start: 0.7971 (tp) cc_final: 0.7753 (tp) REVERT: A 969 PHE cc_start: 0.7693 (m-10) cc_final: 0.7377 (m-10) REVERT: A 1057 MET cc_start: 0.2891 (mmp) cc_final: 0.0527 (pp-130) REVERT: A 1072 THR cc_start: 0.6167 (m) cc_final: 0.5880 (m) REVERT: A 1111 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8174 (mp) REVERT: B 132 HIS cc_start: 0.6059 (OUTLIER) cc_final: 0.4244 (t-170) REVERT: B 285 LYS cc_start: 0.7304 (mmmt) cc_final: 0.6815 (tptp) REVERT: B 408 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: B 442 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7666 (tt) REVERT: C 300 ILE cc_start: 0.8394 (mm) cc_final: 0.8120 (mt) REVERT: C 346 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6621 (mtp) REVERT: C 349 TYR cc_start: 0.5827 (m-10) cc_final: 0.5282 (m-10) REVERT: C 462 MET cc_start: 0.4645 (pp-130) cc_final: 0.4035 (pp-130) REVERT: C 464 GLU cc_start: 0.2536 (OUTLIER) cc_final: 0.2321 (tm-30) outliers start: 36 outliers final: 14 residues processed: 246 average time/residue: 0.5035 time to fit residues: 136.8366 Evaluate side-chains 245 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 464 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS A 970 ASN B 77 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.200949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.177620 restraints weight = 21671.124| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 2.41 r_work: 0.4084 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14047 Z= 0.140 Angle : 0.720 25.523 19224 Z= 0.351 Chirality : 0.063 2.011 2097 Planarity : 0.005 0.046 2340 Dihedral : 16.841 174.772 2149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 3.30 % Allowed : 18.64 % Favored : 78.06 % 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 (0.21), residues: 1611 helix: 0.25 (0.23), residues: 540 sheet: -0.16 (0.40), residues: 160 loop : -1.98 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1142 TYR 0.026 0.001 TYR B 206 PHE 0.024 0.002 PHE A 749 TRP 0.018 0.001 TRP A 607 HIS 0.010 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14047) covalent geometry : angle 0.72018 / 0.35 (19224) hydrogen bonds : bond 0.03863 / 2.67 ( 462) hydrogen bonds : angle 4.62717 / 3.45 ( 1310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 416 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6963 (tp30) REVERT: A 447 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: A 465 ASP cc_start: 0.6770 (m-30) cc_final: 0.6495 (m-30) REVERT: A 478 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6918 (ttp80) REVERT: A 486 TRP cc_start: 0.8128 (p-90) cc_final: 0.7908 (p-90) REVERT: A 1111 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 276 SER cc_start: 0.8254 (m) cc_final: 0.7911 (p) REVERT: B 285 LYS cc_start: 0.7237 (mmmt) cc_final: 0.5669 (mmmm) REVERT: B 442 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7580 (tt) REVERT: C 300 ILE cc_start: 0.8341 (mm) cc_final: 0.8078 (mt) REVERT: C 346 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6456 (mtp) REVERT: C 349 TYR cc_start: 0.5805 (m-10) cc_final: 0.5285 (m-10) REVERT: C 462 MET cc_start: 0.4558 (pp-130) cc_final: 0.4324 (pp-130) REVERT: C 465 MET cc_start: 0.4019 (OUTLIER) cc_final: 0.3747 (tmm) outliers start: 45 outliers final: 19 residues processed: 253 average time/residue: 0.4331 time to fit residues: 121.7476 Evaluate side-chains 250 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 0.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 277 HIS A 420 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.200389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.175524 restraints weight = 28128.913| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 2.87 r_work: 0.4045 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14047 Z= 0.163 Angle : 0.747 25.535 19224 Z= 0.363 Chirality : 0.064 2.011 2097 Planarity : 0.005 0.051 2340 Dihedral : 16.830 174.551 2149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 2.93 % Allowed : 19.52 % Favored : 77.55 % 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 (0.21), residues: 1611 helix: 0.23 (0.23), residues: 546 sheet: -0.16 (0.39), residues: 170 loop : -2.00 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1187 TYR 0.027 0.001 TYR B 206 PHE 0.026 0.002 PHE A 749 TRP 0.017 0.001 TRP A 607 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (14047) covalent geometry : angle 0.74681 / 0.36 (19224) hydrogen bonds : bond 0.03915 / 2.69 ( 462) hydrogen bonds : angle 4.63539 / 3.46 ( 1310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7355 (mp) REVERT: A 416 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7056 (tp30) REVERT: A 447 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7065 (pp20) REVERT: A 465 ASP cc_start: 0.6846 (m-30) cc_final: 0.6574 (m-30) REVERT: A 478 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6938 (ttp80) REVERT: A 486 TRP cc_start: 0.8142 (p-90) cc_final: 0.7931 (p-90) REVERT: A 544 MET cc_start: 0.7293 (mmm) cc_final: 0.7054 (mmm) REVERT: A 1057 MET cc_start: 0.2490 (mmp) cc_final: 0.0582 (pp-130) REVERT: B 132 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.4303 (t-170) REVERT: B 276 SER cc_start: 0.8244 (m) cc_final: 0.7892 (p) REVERT: B 285 LYS cc_start: 0.7333 (mmmt) cc_final: 0.5762 (mmmm) REVERT: B 408 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: B 442 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7626 (tt) REVERT: C 300 ILE cc_start: 0.8390 (mm) cc_final: 0.8130 (mt) REVERT: C 346 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6556 (mtp) REVERT: C 349 TYR cc_start: 0.5914 (m-10) cc_final: 0.5330 (m-10) REVERT: C 464 GLU cc_start: 0.2671 (OUTLIER) cc_final: 0.2423 (tt0) outliers start: 40 outliers final: 24 residues processed: 247 average time/residue: 0.4640 time to fit residues: 127.0038 Evaluate side-chains 252 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 464 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.0970 chunk 153 optimal weight: 0.0030 chunk 135 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 10 optimal weight: 0.0050 chunk 88 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 134 ASN A 277 HIS A1102 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.201714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.178851 restraints weight = 21653.885| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.39 r_work: 0.4104 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14047 Z= 0.129 Angle : 0.731 25.531 19224 Z= 0.353 Chirality : 0.063 2.011 2097 Planarity : 0.005 0.051 2340 Dihedral : 16.758 174.539 2149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.06 % Favored : 89.88 % Rotamer: Outliers : 2.20 % Allowed : 20.18 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.21), residues: 1611 helix: 0.38 (0.23), residues: 543 sheet: -0.12 (0.39), residues: 170 loop : -1.99 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1187 TYR 0.024 0.001 TYR B 206 PHE 0.026 0.001 PHE A 749 TRP 0.013 0.001 TRP A 607 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14047) covalent geometry : angle 0.73107 / 0.35 (19224) hydrogen bonds : bond 0.03674 / 2.54 ( 462) hydrogen bonds : angle 4.53865 / 3.39 ( 1310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7046 (pmm) cc_final: 0.6661 (ptp) REVERT: A 141 LEU cc_start: 0.7440 (mm) cc_final: 0.6948 (mm) REVERT: A 245 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 416 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6973 (tp30) REVERT: A 447 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: A 465 ASP cc_start: 0.6758 (m-30) cc_final: 0.6484 (m-30) REVERT: A 478 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6782 (ttp80) REVERT: A 544 MET cc_start: 0.7268 (mmm) cc_final: 0.7043 (mmm) REVERT: A 1057 MET cc_start: 0.2383 (mmp) cc_final: 0.0607 (pp-130) REVERT: B 276 SER cc_start: 0.8187 (m) cc_final: 0.7843 (p) REVERT: B 285 LYS cc_start: 0.7287 (mmmt) cc_final: 0.6788 (mmmt) REVERT: B 442 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7539 (tt) REVERT: C 346 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6397 (mtp) REVERT: C 349 TYR cc_start: 0.5830 (m-10) cc_final: 0.5278 (m-10) outliers start: 30 outliers final: 16 residues processed: 245 average time/residue: 0.4970 time to fit residues: 134.9441 Evaluate side-chains 246 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS A 740 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.198829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176244 restraints weight = 19224.632| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.22 r_work: 0.4072 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14047 Z= 0.188 Angle : 0.793 25.510 19224 Z= 0.383 Chirality : 0.064 2.014 2097 Planarity : 0.005 0.051 2340 Dihedral : 16.820 174.059 2149 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.17 % Favored : 88.76 % Rotamer: Outliers : 2.35 % Allowed : 20.84 % Favored : 76.82 % 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: -1.52 (0.21), residues: 1611 helix: 0.16 (0.23), residues: 548 sheet: -0.20 (0.39), residues: 170 loop : -2.01 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 107 TYR 0.030 0.002 TYR B 206 PHE 0.027 0.002 PHE A 749 TRP 0.040 0.002 TRP A 486 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (14047) covalent geometry : angle 0.79304 / 0.38 (19224) hydrogen bonds : bond 0.04121 / 2.85 ( 462) hydrogen bonds : angle 4.69658 / 3.51 ( 1310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7637 (mm) cc_final: 0.7082 (mm) REVERT: A 245 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7464 (mp) REVERT: A 416 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7332 (tp30) REVERT: A 447 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: A 465 ASP cc_start: 0.7018 (m-30) cc_final: 0.6753 (m-30) REVERT: A 478 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6786 (ttp80) REVERT: A 488 LEU cc_start: 0.8421 (mt) cc_final: 0.8132 (mp) REVERT: A 544 MET cc_start: 0.7570 (mmm) cc_final: 0.7281 (mmm) REVERT: A 592 LEU cc_start: 0.7023 (tp) cc_final: 0.6770 (mt) REVERT: A 1102 GLN cc_start: 0.7958 (mt0) cc_final: 0.7617 (mt0) REVERT: B 276 SER cc_start: 0.8254 (m) cc_final: 0.7920 (p) REVERT: B 285 LYS cc_start: 0.7506 (mmmt) cc_final: 0.5867 (mmmm) REVERT: B 442 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7747 (tt) REVERT: C 346 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6849 (mtp) REVERT: C 349 TYR cc_start: 0.6291 (m-10) cc_final: 0.5630 (m-10) outliers start: 32 outliers final: 20 residues processed: 251 average time/residue: 0.4933 time to fit residues: 137.6724 Evaluate side-chains 253 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 740 ASN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 122 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.198744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.175302 restraints weight = 22241.375| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.45 r_work: 0.4053 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 14047 Z= 0.220 Angle : 0.994 59.200 19224 Z= 0.538 Chirality : 0.063 2.014 2097 Planarity : 0.005 0.057 2340 Dihedral : 16.823 174.076 2149 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.24 % Favored : 88.70 % Rotamer: Outliers : 1.91 % Allowed : 21.64 % Favored : 76.45 % Cbeta Deviations : 0.07 % 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: -1.52 (0.21), residues: 1611 helix: 0.16 (0.23), residues: 548 sheet: -0.20 (0.39), residues: 170 loop : -2.02 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 107 TYR 0.030 0.002 TYR B 206 PHE 0.026 0.002 PHE A 749 TRP 0.034 0.002 TRP A 486 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 (14047) covalent geometry : angle 0.99426 / 0.54 (19224) hydrogen bonds : bond 0.04107 / 2.84 ( 462) hydrogen bonds : angle 4.69601 / 3.51 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.02 seconds wall clock time: 78 minutes 35.41 seconds (4715.41 seconds total)