Starting phenix.real_space_refine on Thu Aug 6 04:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5k_29747/08_2026/8g5k_29747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5k_29747/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2026/8g5k_29747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2026/8g5k_29747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2026/8g5k_29747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2026/8g5k_29747.map" } 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-2.2rc3-6140/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: 2.67, per 1000 atoms: 0.20 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: 1.18 Conformation dependent library (CDL) restraints added in 612.8 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: 1.48 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: 2.05 Time building geometry restraints manager: 1.48 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 119.70 106.52 13.18 1.20e+00 6.94e-01 1.21e+02 angle pdb=" C3' DC P 25 " pdb=" O3' DC P 25 " pdb=" P DG P 26 " ideal model delta sigma weight residual 119.70 109.08 10.62 1.20e+00 6.94e-01 7.83e+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 ... (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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- 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= 0.592 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 1.08634 / 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 : 0.296 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: 0.4309 time to fit residues: 126.3722 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 : 0.467 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS 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 = 0.4578 r_free = 0.4578 target = 0.212659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.189391 restraints weight = 22520.679| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.40 r_work: 0.4240 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4245 r_free = 0.4245 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14047 Z= 0.163 Angle : 0.768 24.150 19224 Z= 0.371 Chirality : 0.064 2.051 2097 Planarity : 0.005 0.070 2340 Dihedral : 16.891 175.090 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 2.35 % Allowed : 9.61 % Favored : 88.04 % 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: -1.39 (0.20), residues: 1611 helix: 0.46 (0.23), residues: 519 sheet: -0.25 (0.36), residues: 187 loop : -2.00 (0.20), residues: 905 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 0.00345 / 0.16 (14047) covalent geometry : angle 0.76849 / 0.37 (19224) hydrogen bonds : bond 0.04319 / 2.94 ( 462) hydrogen bonds : angle 4.76641 / 3.68 ( 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 268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 100 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (m) REVERT: A 220 TRP cc_start: 0.5229 (m100) cc_final: 0.4685 (m100) REVERT: A 465 ASP cc_start: 0.6954 (m-30) cc_final: 0.6717 (m-30) REVERT: A 544 MET cc_start: 0.6947 (mmm) cc_final: 0.6674 (mmm) REVERT: A 953 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6162 (mtm110) REVERT: A 1057 MET cc_start: 0.4110 (mmm) cc_final: 0.1953 (ptm) REVERT: A 1107 ASP cc_start: 0.6433 (m-30) cc_final: 0.6211 (m-30) REVERT: B 241 TRP cc_start: 0.7267 (t-100) cc_final: 0.7065 (t-100) REVERT: B 256 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 458 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7762 (ttp-170) REVERT: C 300 ILE cc_start: 0.8280 (mm) cc_final: 0.8007 (mt) outliers start: 32 outliers final: 12 residues processed: 244 average time/residue: 0.4416 time to fit residues: 118.9256 Evaluate side-chains 236 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 221 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 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 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1206 MET 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: 0.9980 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 158 optimal weight: 9.9990 chunk 75 optimal weight: 0.0770 chunk 139 optimal weight: 0.0980 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** C 305 ASN ** 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 = 0.4573 r_free = 0.4573 target = 0.212298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.189424 restraints weight = 20502.806| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.27 r_work: 0.4230 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4236 r_free = 0.4236 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4236 r_free = 0.4236 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1837 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= 0.126 Angle : 0.704 24.989 19224 Z= 0.339 Chirality : 0.063 2.018 2097 Planarity : 0.005 0.056 2340 Dihedral : 16.773 176.021 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.06 % Favored : 90.88 % Rotamer: Outliers : 2.86 % Allowed : 12.03 % Favored : 85.11 % 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: -1.26 (0.21), residues: 1611 helix: 0.62 (0.23), residues: 529 sheet: -0.24 (0.37), residues: 178 loop : -1.95 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 866 TYR 0.022 0.001 TYR B 206 PHE 0.024 0.001 PHE A 749 TRP 0.012 0.001 TRP A 607 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (14047) covalent geometry : angle 0.70400 / 0.34 (19224) hydrogen bonds : bond 0.03791 / 2.61 ( 462) hydrogen bonds : angle 4.45823 / 3.41 ( 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 259 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 100 VAL cc_start: 0.7321 (OUTLIER) cc_final: 0.7100 (m) REVERT: A 465 ASP cc_start: 0.6901 (m-30) cc_final: 0.6658 (m-30) REVERT: A 544 MET cc_start: 0.6890 (mmm) cc_final: 0.6621 (mmm) REVERT: A 953 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.6190 (mtm110) REVERT: A 985 MET cc_start: 0.4452 (mmt) cc_final: 0.2807 (mmt) REVERT: A 1057 MET cc_start: 0.4128 (mmm) cc_final: 0.1713 (ptm) REVERT: A 1107 ASP cc_start: 0.6399 (m-30) cc_final: 0.6183 (m-30) REVERT: B 241 TRP cc_start: 0.7256 (t-100) cc_final: 0.6904 (t-100) REVERT: B 260 LEU cc_start: 0.7523 (tp) cc_final: 0.7203 (mt) REVERT: C 300 ILE cc_start: 0.8266 (mm) cc_final: 0.8033 (mt) REVERT: C 346 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6101 (mtp) outliers start: 39 outliers final: 16 residues processed: 231 average time/residue: 0.4354 time to fit residues: 111.8025 Evaluate side-chains 238 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 290 ARG Chi-restraints excluded: chain A residue 310 SER 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 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 442 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 346 MET 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: 0.3980 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.205367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.181687 restraints weight = 21860.363| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 2.41 r_work: 0.4150 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4155 r_free = 0.4155 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14047 Z= 0.188 Angle : 0.765 25.023 19224 Z= 0.373 Chirality : 0.065 2.021 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.931 174.802 2149 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.06 % Favored : 89.82 % Rotamer: Outliers : 2.79 % Allowed : 14.23 % Favored : 82.98 % 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: -1.49 (0.20), residues: 1611 helix: 0.24 (0.22), residues: 544 sheet: -0.12 (0.37), residues: 185 loop : -2.07 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 259 TYR 0.032 0.002 TYR B 206 PHE 0.025 0.002 PHE A 749 TRP 0.021 0.002 TRP A 607 HIS 0.011 0.002 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (14047) covalent geometry : angle 0.76539 / 0.37 (19224) hydrogen bonds : bond 0.04258 / 2.93 ( 462) hydrogen bonds : angle 4.69166 / 3.51 ( 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 281 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 243 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7317 (mtt) REVERT: A 416 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6887 (tp30) REVERT: A 465 ASP cc_start: 0.6896 (m-30) cc_final: 0.6657 (m-30) REVERT: A 544 MET cc_start: 0.6923 (mmm) cc_final: 0.6593 (mmm) REVERT: A 803 ASN cc_start: 0.7587 (t0) cc_final: 0.7342 (t0) REVERT: A 953 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6143 (mtm110) REVERT: A 965 LEU cc_start: 0.7831 (tp) cc_final: 0.7612 (tp) REVERT: A 969 PHE cc_start: 0.7576 (m-10) cc_final: 0.7310 (m-10) REVERT: A 1111 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (mp) REVERT: C 300 ILE cc_start: 0.8434 (mm) cc_final: 0.8212 (mt) REVERT: C 346 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6430 (mtp) REVERT: C 382 LYS cc_start: 0.5413 (OUTLIER) cc_final: 0.5064 (mppt) REVERT: C 462 MET cc_start: 0.4154 (pp-130) cc_final: 0.3537 (pp-130) outliers start: 38 outliers final: 16 residues processed: 258 average time/residue: 0.4867 time to fit residues: 138.0281 Evaluate side-chains 252 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 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 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 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL 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 337 SER Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 382 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 123 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 409 ASN C 192 HIS ** C 305 ASN ** 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 = 0.4469 r_free = 0.4469 target = 0.201405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175991 restraints weight = 28596.720| |-----------------------------------------------------------------------------| r_work (start): 0.4171 rms_B_bonded: 2.91 r_work: 0.4050 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14047 Z= 0.207 Angle : 0.766 25.141 19224 Z= 0.377 Chirality : 0.065 2.012 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.957 175.564 2149 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.18 % Favored : 89.70 % Rotamer: Outliers : 3.89 % Allowed : 15.63 % Favored : 80.48 % 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: -1.63 (0.20), residues: 1611 helix: 0.04 (0.22), residues: 545 sheet: -0.19 (0.38), residues: 179 loop : -2.09 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.027 0.002 TYR B 206 PHE 0.023 0.002 PHE A 749 TRP 0.022 0.002 TRP A 607 HIS 0.034 0.002 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (14047) covalent geometry : angle 0.76567 / 0.38 (19224) hydrogen bonds : bond 0.04271 / 2.93 ( 462) hydrogen bonds : angle 4.75683 / 3.55 ( 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 295 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.427 Fit side-chains REVERT: A 86 GLN cc_start: 0.6123 (mm-40) cc_final: 0.5595 (mm-40) REVERT: A 290 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7945 (mmt-90) REVERT: A 297 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7442 (mtt) REVERT: A 390 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: A 465 ASP cc_start: 0.6908 (m-30) cc_final: 0.6614 (m-30) REVERT: A 478 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6971 (ttp80) REVERT: A 486 TRP cc_start: 0.8136 (p-90) cc_final: 0.7853 (p-90) REVERT: A 544 MET cc_start: 0.6993 (mmm) cc_final: 0.6637 (mmm) REVERT: A 597 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7377 (mtt180) REVERT: A 803 ASN cc_start: 0.7591 (t0) cc_final: 0.7366 (t0) REVERT: A 898 ILE cc_start: 0.7525 (mm) cc_final: 0.7306 (mm) REVERT: A 953 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6167 (mtm110) REVERT: A 1072 THR cc_start: 0.6127 (m) cc_final: 0.5875 (m) REVERT: A 1111 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 1138 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7049 (mmt-90) REVERT: B 285 LYS cc_start: 0.7318 (tptp) cc_final: 0.7059 (tptp) REVERT: B 442 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7612 (tt) REVERT: C 300 ILE cc_start: 0.8440 (mm) cc_final: 0.8212 (mt) REVERT: C 346 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6602 (mtp) REVERT: C 349 TYR cc_start: 0.5670 (m-10) cc_final: 0.5166 (m-10) REVERT: C 382 LYS cc_start: 0.5500 (OUTLIER) cc_final: 0.5100 (mppt) outliers start: 53 outliers final: 22 residues processed: 264 average time/residue: 0.4654 time to fit residues: 135.9739 Evaluate side-chains 268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 478 ARG 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 778 THR 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 1111 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 132 HIS 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 442 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 298 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 79 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.201436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.176213 restraints weight = 28293.059| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.89 r_work: 0.4048 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4054 r_free = 0.4054 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14047 Z= 0.169 Angle : 0.752 25.132 19224 Z= 0.367 Chirality : 0.064 2.012 2097 Planarity : 0.005 0.047 2340 Dihedral : 16.902 175.263 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.49 % Favored : 89.39 % Rotamer: Outliers : 3.37 % Allowed : 17.53 % Favored : 79.09 % 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: -1.57 (0.21), residues: 1611 helix: 0.17 (0.23), residues: 544 sheet: -0.30 (0.38), residues: 179 loop : -2.07 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 126 TYR 0.026 0.002 TYR B 206 PHE 0.021 0.002 PHE A 749 TRP 0.019 0.002 TRP A 607 HIS 0.005 0.001 HIS A 805 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (14047) covalent geometry : angle 0.75190 / 0.37 (19224) hydrogen bonds : bond 0.04019 / 2.77 ( 462) hydrogen bonds : angle 4.68696 / 3.49 ( 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 284 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.281 Fit side-chains REVERT: A 245 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7166 (mp) REVERT: A 465 ASP cc_start: 0.6844 (m-30) cc_final: 0.6592 (m-30) REVERT: A 486 TRP cc_start: 0.8126 (p-90) cc_final: 0.7839 (p-90) REVERT: A 544 MET cc_start: 0.7004 (mmm) cc_final: 0.6635 (mmm) REVERT: A 803 ASN cc_start: 0.7598 (t0) cc_final: 0.7371 (t0) REVERT: A 898 ILE cc_start: 0.7436 (mm) cc_final: 0.7218 (mm) REVERT: A 953 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6126 (mtm110) REVERT: A 1111 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 442 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7581 (tt) REVERT: C 300 ILE cc_start: 0.8404 (mm) cc_final: 0.8172 (mt) REVERT: C 346 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6596 (mtp) REVERT: C 349 TYR cc_start: 0.5735 (m-10) cc_final: 0.5286 (m-10) REVERT: C 382 LYS cc_start: 0.5398 (OUTLIER) cc_final: 0.4647 (mptp) REVERT: C 462 MET cc_start: 0.4114 (ppp) cc_final: 0.3857 (ppp) outliers start: 46 outliers final: 27 residues processed: 260 average time/residue: 0.4344 time to fit residues: 124.9857 Evaluate side-chains 264 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 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 856 GLU Chi-restraints excluded: chain A residue 953 ARG 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 91 LEU Chi-restraints excluded: chain B residue 132 HIS 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 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 117 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 1.9990 chunk 115 optimal weight: 0.0370 chunk 49 optimal weight: 0.0870 chunk 160 optimal weight: 0.0060 chunk 30 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.1290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 440 ASN A 541 GLN A 970 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** 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 = 0.4492 r_free = 0.4492 target = 0.203520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.179961 restraints weight = 21767.755| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 2.43 r_work: 0.4137 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14047 Z= 0.124 Angle : 0.715 25.155 19224 Z= 0.348 Chirality : 0.063 2.010 2097 Planarity : 0.005 0.050 2340 Dihedral : 16.799 175.706 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.62 % Favored : 90.32 % Rotamer: Outliers : 2.57 % Allowed : 19.22 % Favored : 78.21 % 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: 0.43 (0.23), residues: 538 sheet: -0.20 (0.39), residues: 173 loop : -2.00 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1187 TYR 0.022 0.001 TYR B 206 PHE 0.019 0.001 PHE A 749 TRP 0.013 0.001 TRP A 607 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14047) covalent geometry : angle 0.71512 / 0.35 (19224) hydrogen bonds : bond 0.03628 / 2.52 ( 462) hydrogen bonds : angle 4.52271 / 3.37 ( 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 263 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7175 (mp) REVERT: A 465 ASP cc_start: 0.6755 (m-30) cc_final: 0.6469 (m-30) REVERT: A 486 TRP cc_start: 0.8047 (p-90) cc_final: 0.7792 (p-90) REVERT: A 544 MET cc_start: 0.7009 (mmm) cc_final: 0.6621 (mmm) REVERT: A 803 ASN cc_start: 0.7551 (t0) cc_final: 0.7345 (t160) REVERT: A 898 ILE cc_start: 0.7414 (mm) cc_final: 0.7194 (mm) REVERT: A 953 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.6058 (ttp80) REVERT: A 969 PHE cc_start: 0.7578 (m-10) cc_final: 0.7314 (m-10) REVERT: A 1057 MET cc_start: 0.2194 (mmp) cc_final: 0.0296 (pp-130) REVERT: B 276 SER cc_start: 0.8234 (m) cc_final: 0.7846 (p) REVERT: B 408 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: B 442 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7500 (tt) REVERT: C 300 ILE cc_start: 0.8366 (mm) cc_final: 0.8127 (mt) REVERT: C 346 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6432 (mtp) outliers start: 35 outliers final: 17 residues processed: 244 average time/residue: 0.4385 time to fit residues: 118.3100 Evaluate side-chains 244 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE 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 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 LEU 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 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE 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 298 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 411 ILE 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: 2.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 0.0570 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.197973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172865 restraints weight = 27973.217| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.87 r_work: 0.4016 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (14 function evaluations) r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14047 Z= 0.223 Angle : 0.816 25.178 19224 Z= 0.400 Chirality : 0.066 2.013 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.934 174.754 2149 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.24 % Favored : 88.70 % Rotamer: Outliers : 3.45 % Allowed : 19.08 % Favored : 77.48 % 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: -1.66 (0.20), residues: 1611 helix: -0.01 (0.22), residues: 550 sheet: -0.25 (0.38), residues: 183 loop : -2.09 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 597 TYR 0.033 0.002 TYR B 206 PHE 0.029 0.002 PHE A 749 TRP 0.024 0.002 TRP A 607 HIS 0.012 0.002 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (14047) covalent geometry : angle 0.81591 / 0.40 (19224) hydrogen bonds : bond 0.04482 / 3.09 ( 462) hydrogen bonds : angle 4.84608 / 3.61 ( 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 287 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.415 Fit side-chains REVERT: A 141 LEU cc_start: 0.7407 (mm) cc_final: 0.6891 (mm) REVERT: A 390 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: A 447 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6772 (pp20) REVERT: A 465 ASP cc_start: 0.6856 (m-30) cc_final: 0.6591 (m-30) REVERT: A 486 TRP cc_start: 0.8198 (p-90) cc_final: 0.7935 (p-90) REVERT: A 544 MET cc_start: 0.7096 (mmm) cc_final: 0.6701 (mmm) REVERT: A 953 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6176 (mtm110) REVERT: A 1057 MET cc_start: 0.2165 (mmp) cc_final: 0.0781 (pp-130) REVERT: B 113 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7855 (mt-10) REVERT: B 132 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.4449 (t-170) REVERT: B 276 SER cc_start: 0.8211 (m) cc_final: 0.7856 (p) REVERT: B 442 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 300 ILE cc_start: 0.8441 (mm) cc_final: 0.8235 (mt) REVERT: C 346 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6731 (mtp) REVERT: C 349 TYR cc_start: 0.5969 (m-10) cc_final: 0.5388 (m-10) outliers start: 47 outliers final: 22 residues processed: 263 average time/residue: 0.4146 time to fit residues: 120.8958 Evaluate side-chains 262 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 390 GLN 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 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 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 953 ARG 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 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 298 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 10 optimal weight: 0.0570 chunk 88 optimal weight: 0.0980 chunk 162 optimal weight: 9.9990 chunk 148 optimal weight: 0.0770 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN A 440 ASN A 803 ASN A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.201674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.178214 restraints weight = 21658.240| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.43 r_work: 0.4122 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14047 Z= 0.135 Angle : 0.757 25.176 19224 Z= 0.366 Chirality : 0.063 2.009 2097 Planarity : 0.005 0.055 2340 Dihedral : 16.791 175.329 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.75 % Favored : 90.19 % Rotamer: Outliers : 2.27 % Allowed : 20.18 % 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: -1.43 (0.21), residues: 1611 helix: 0.36 (0.23), residues: 537 sheet: -0.28 (0.38), residues: 185 loop : -2.01 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1187 TYR 0.024 0.001 TYR B 206 PHE 0.028 0.001 PHE A 749 TRP 0.016 0.001 TRP A1118 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (14047) covalent geometry : angle 0.75685 / 0.37 (19224) hydrogen bonds : bond 0.03754 / 2.61 ( 462) hydrogen bonds : angle 4.62602 / 3.45 ( 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 255 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.6991 (pmm) cc_final: 0.6592 (ptp) REVERT: A 141 LEU cc_start: 0.7443 (mm) cc_final: 0.6964 (mm) REVERT: A 299 MET cc_start: 0.7350 (mmm) cc_final: 0.6802 (tpt) REVERT: A 447 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6760 (pp20) REVERT: A 465 ASP cc_start: 0.6746 (m-30) cc_final: 0.6445 (m-30) REVERT: A 478 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6898 (ttp80) REVERT: A 486 TRP cc_start: 0.8133 (p-90) cc_final: 0.7914 (p-90) REVERT: A 953 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.6013 (ttp80) REVERT: A 1057 MET cc_start: 0.1966 (mmp) cc_final: 0.0558 (pp-130) REVERT: B 276 SER cc_start: 0.8190 (m) cc_final: 0.7811 (p) REVERT: B 442 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7517 (tt) REVERT: C 300 ILE cc_start: 0.8371 (mm) cc_final: 0.8147 (mt) REVERT: C 346 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6479 (mtp) REVERT: C 349 TYR cc_start: 0.5918 (m-10) cc_final: 0.5354 (m-10) outliers start: 31 outliers final: 18 residues processed: 239 average time/residue: 0.4433 time to fit residues: 118.0121 Evaluate side-chains 243 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 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 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 LEU 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 1141 VAL 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 383 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 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: 0.7980 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 139 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.200344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.177797 restraints weight = 19211.156| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 2.22 r_work: 0.4118 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14047 Z= 0.158 Angle : 0.758 25.178 19224 Z= 0.367 Chirality : 0.064 2.009 2097 Planarity : 0.005 0.050 2340 Dihedral : 16.792 174.895 2149 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 2.27 % Allowed : 20.32 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1611 helix: 0.27 (0.23), residues: 544 sheet: -0.21 (0.39), residues: 169 loop : -1.98 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1187 TYR 0.027 0.001 TYR B 206 PHE 0.029 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 0.00352 / 0.16 (14047) covalent geometry : angle 0.75753 / 0.37 (19224) hydrogen bonds : bond 0.03839 / 2.65 ( 462) hydrogen bonds : angle 4.68688 / 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 262 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 141 LEU cc_start: 0.7588 (mm) cc_final: 0.7063 (mm) REVERT: A 299 MET cc_start: 0.7441 (mmm) cc_final: 0.6918 (tpt) REVERT: A 390 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: A 447 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: A 465 ASP cc_start: 0.7017 (m-30) cc_final: 0.6744 (m-30) REVERT: A 478 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6837 (ttp80) REVERT: A 486 TRP cc_start: 0.8162 (p-90) cc_final: 0.7890 (p-90) REVERT: A 544 MET cc_start: 0.7657 (mmm) cc_final: 0.7361 (mmm) REVERT: A 953 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6164 (ttp80) REVERT: A 1057 MET cc_start: 0.2160 (mmp) cc_final: 0.0678 (pp-130) REVERT: B 132 HIS cc_start: 0.6120 (OUTLIER) cc_final: 0.4415 (t-170) REVERT: B 276 SER cc_start: 0.8253 (m) cc_final: 0.7892 (p) REVERT: B 442 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7679 (tt) REVERT: C 300 ILE cc_start: 0.8487 (mm) cc_final: 0.8268 (mt) REVERT: C 346 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6830 (mtp) REVERT: C 349 TYR cc_start: 0.6307 (m-10) cc_final: 0.5634 (m-10) outliers start: 31 outliers final: 20 residues processed: 245 average time/residue: 0.4265 time to fit residues: 115.8271 Evaluate side-chains 252 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 390 GLN 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 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 592 LEU 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 858 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 91 LEU 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 370 LYS 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 298 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 122 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN ** B 77 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 = 0.4461 r_free = 0.4461 target = 0.200408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.176980 restraints weight = 22183.783| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.45 r_work: 0.4102 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 14047 Z= 0.215 Angle : 0.975 59.113 19224 Z= 0.531 Chirality : 0.064 2.009 2097 Planarity : 0.005 0.060 2340 Dihedral : 16.796 174.901 2149 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.92 % Favored : 89.01 % Rotamer: Outliers : 1.98 % Allowed : 20.62 % Favored : 77.40 % 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: -1.45 (0.21), residues: 1611 helix: 0.27 (0.23), residues: 544 sheet: -0.22 (0.39), residues: 169 loop : -1.99 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1187 TYR 0.026 0.001 TYR B 206 PHE 0.028 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 0.00442 / 0.21 (14047) covalent geometry : angle 0.97539 / 0.53 (19224) hydrogen bonds : bond 0.03833 / 2.64 ( 462) hydrogen bonds : angle 4.68618 / 3.51 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4033.89 seconds wall clock time: 69 minutes 18.25 seconds (4158.25 seconds total)