Starting phenix.real_space_refine on Sat Aug 23 17:23:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5k_29747/08_2025/8g5k_29747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5k_29747/08_2025/8g5k_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_2025/8g5k_29747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2025/8g5k_29747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2025/8g5k_29747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5k_29747/08_2025/8g5k_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-2.0-5787/lib/python3.9/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: 2.79, 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: 0.94 Conformation dependent library (CDL) restraints added in 502.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.39 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: 1.72 Time building geometry restraints manager: 1.22 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=" 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=" N VAL A 353 " pdb=" CA VAL A 353 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N GLU B 282 " pdb=" CA GLU B 282 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.74e+00 bond pdb=" N ILE A 313 " pdb=" CA ILE A 313 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.18e-02 7.18e+03 7.39e+00 bond pdb=" C3' DA P 10 " pdb=" O3' DA P 10 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.55e+00 ... (remaining 14042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 19095 5.20 - 10.40: 111 10.40 - 15.60: 14 15.60 - 20.80: 2 20.80 - 26.00: 2 Bond angle restraints: 19224 Sorted by residual: angle pdb=" C3' DG P 24 " pdb=" O3' DG P 24 " pdb=" P DC P 25 " ideal model delta sigma weight residual 120.20 106.52 13.68 1.50e+00 4.44e-01 8.32e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP2 DG P 11 " ideal model delta sigma weight residual 108.00 82.00 26.00 3.00e+00 1.11e-01 7.51e+01 angle pdb=" N PRO A 241 " pdb=" CD PRO A 241 " pdb=" CG PRO A 241 " ideal model delta sigma weight residual 103.20 90.30 12.90 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N PRO A 241 " pdb=" CA PRO A 241 " pdb=" CB PRO A 241 " ideal model delta sigma weight residual 103.25 94.97 8.28 1.05e+00 9.07e-01 6.22e+01 angle pdb=" O3' DA P 10 " pdb=" P DG P 11 " pdb=" OP1 DG P 11 " ideal model delta sigma weight residual 108.00 84.73 23.27 3.00e+00 1.11e-01 6.01e+01 ... (remaining 19219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8017 35.44 - 70.88: 209 70.88 - 106.32: 12 106.32 - 141.76: 2 141.76 - 177.20: 3 Dihedral angle restraints: 8243 sinusoidal: 3527 harmonic: 4716 Sorted by residual: dihedral pdb=" CD ARG A 309 " pdb=" NE ARG A 309 " pdb=" CZ ARG A 309 " pdb=" NH1 ARG A 309 " ideal model delta sinusoidal sigma weight residual 0.00 74.98 -74.98 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CA LEU B 106 " pdb=" C LEU B 106 " pdb=" N ARG B 107 " pdb=" CA ARG B 107 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 8240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.416: 2091 0.416 - 0.831: 5 0.831 - 1.247: 0 1.247 - 1.662: 0 1.662 - 2.078: 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 2.35 0.27 2.08 2.00e-01 2.50e+01 1.08e+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 2.35 2.98 -0.64 2.00e-01 2.50e+01 1.02e+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 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.73e+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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 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= 0.242 Angle : 1.073 25.995 19224 Z= 0.550 Chirality : 0.075 2.078 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 aren 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 covalent geometry : bond 0.00468 (14047) covalent geometry : angle 1.07339 (19224) hydrogen bonds : bond 0.13107 ( 462) hydrogen bonds : angle 5.86470 ( 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 : 0.408 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: 0.5498 time to fit residues: 160.2874 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 : 0.506 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 323 HIS B 375 HIS B 404 ASN C 133 HIS C 422 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.210540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187013 restraints weight = 22375.033| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.42 r_work: 0.4205 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.1821 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= 0.168 Angle : 0.761 26.562 19224 Z= 0.364 Chirality : 0.062 1.981 2097 Planarity : 0.005 0.058 2340 Dihedral : 16.822 176.803 2149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 2.57 % Allowed : 9.46 % Favored : 87.97 % 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 aren not related in a simple way. whole: -1.38 (0.20), residues: 1611 helix: 0.36 (0.23), residues: 537 sheet: -0.17 (0.36), residues: 187 loop : -1.99 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 309 TYR 0.026 0.002 TYR B 206 PHE 0.024 0.002 PHE A 749 TRP 0.021 0.002 TRP A 607 HIS 0.006 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00376 (14047) covalent geometry : angle 0.76060 (19224) hydrogen bonds : bond 0.04088 ( 462) hydrogen bonds : angle 4.63981 ( 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 280 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 100 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.7183 (m) REVERT: A 220 TRP cc_start: 0.5491 (m100) cc_final: 0.5263 (m100) REVERT: A 465 ASP cc_start: 0.6975 (m-30) cc_final: 0.6690 (m-30) REVERT: A 486 TRP cc_start: 0.7831 (p-90) cc_final: 0.7625 (p-90) REVERT: A 544 MET cc_start: 0.6942 (mmm) cc_final: 0.6657 (mmm) REVERT: A 953 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6238 (mtm110) REVERT: A 1057 MET cc_start: 0.3965 (mmm) cc_final: 0.1736 (ptm) REVERT: A 1107 ASP cc_start: 0.6495 (m-30) cc_final: 0.6277 (m-30) REVERT: B 260 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7297 (mt) REVERT: B 404 ASN cc_start: 0.7642 (m-40) cc_final: 0.7428 (m-40) REVERT: B 458 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7726 (ttp-170) REVERT: C 300 ILE cc_start: 0.8310 (mm) cc_final: 0.8055 (mt) outliers start: 35 outliers final: 11 residues processed: 255 average time/residue: 0.5867 time to fit residues: 164.3949 Evaluate side-chains 242 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 873 GLU Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 298 GLU 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: 1.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 354 ASN A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.206202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.183006 restraints weight = 19985.406| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.31 r_work: 0.4167 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14047 Z= 0.160 Angle : 0.718 25.853 19224 Z= 0.347 Chirality : 0.062 2.001 2097 Planarity : 0.005 0.051 2340 Dihedral : 16.768 177.728 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.50 % Favored : 90.38 % Rotamer: Outliers : 3.01 % Allowed : 13.57 % Favored : 83.42 % 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 aren not related in a simple way. whole: -1.29 (0.21), residues: 1611 helix: 0.46 (0.23), residues: 538 sheet: 0.04 (0.37), residues: 172 loop : -1.96 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 866 TYR 0.027 0.001 TYR B 206 PHE 0.026 0.002 PHE A 749 TRP 0.015 0.001 TRP A 607 HIS 0.008 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00354 (14047) covalent geometry : angle 0.71842 (19224) hydrogen bonds : bond 0.03736 ( 462) hydrogen bonds : angle 4.52823 ( 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 276 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7856 (mpt180) REVERT: A 297 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6951 (mtt) REVERT: A 465 ASP cc_start: 0.6900 (m-30) cc_final: 0.6607 (m-30) REVERT: A 544 MET cc_start: 0.6951 (mmm) cc_final: 0.6636 (mmm) REVERT: A 953 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.6153 (mtm110) REVERT: A 965 LEU cc_start: 0.7754 (tp) cc_final: 0.7521 (tp) REVERT: A 969 PHE cc_start: 0.7475 (m-10) cc_final: 0.7245 (m-10) REVERT: A 1107 ASP cc_start: 0.6639 (m-30) cc_final: 0.6418 (m-30) REVERT: B 404 ASN cc_start: 0.7781 (m-40) cc_final: 0.7532 (m110) REVERT: B 442 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7597 (tp) REVERT: C 300 ILE cc_start: 0.8346 (mm) cc_final: 0.8113 (mt) REVERT: C 346 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6346 (mtp) REVERT: C 382 LYS cc_start: 0.5399 (OUTLIER) cc_final: 0.4984 (mppt) REVERT: C 462 MET cc_start: 0.3981 (pp-130) cc_final: 0.3327 (pp-130) outliers start: 41 outliers final: 15 residues processed: 248 average time/residue: 0.5850 time to fit residues: 159.6548 Evaluate side-chains 249 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 25 optimal weight: 0.0170 chunk 161 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 overall best weight: 0.7234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.204215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.180909 restraints weight = 21952.136| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.41 r_work: 0.4147 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4152 r_free = 0.4152 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4152 r_free = 0.4152 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.2883 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= 0.161 Angle : 0.709 25.996 19224 Z= 0.343 Chirality : 0.062 1.993 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.777 177.734 2149 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.75 % Favored : 90.13 % Rotamer: Outliers : 2.93 % Allowed : 15.11 % Favored : 81.95 % 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 aren not related in a simple way. whole: -1.29 (0.21), residues: 1611 helix: 0.48 (0.23), residues: 531 sheet: 0.06 (0.38), residues: 171 loop : -1.96 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.026 0.001 TYR B 206 PHE 0.026 0.002 PHE A 749 TRP 0.016 0.001 TRP A 607 HIS 0.006 0.001 HIS A 805 Details of bonding type rmsd covalent geometry : bond 0.00362 (14047) covalent geometry : angle 0.70930 (19224) hydrogen bonds : bond 0.03693 ( 462) hydrogen bonds : angle 4.49844 ( 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 278 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.507 Fit side-chains REVERT: A 141 LEU cc_start: 0.7534 (mm) cc_final: 0.7191 (mm) REVERT: A 297 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7256 (mtt) REVERT: A 465 ASP cc_start: 0.6743 (m-30) cc_final: 0.6499 (m-30) REVERT: A 486 TRP cc_start: 0.8040 (p-90) cc_final: 0.7718 (p-90) REVERT: A 544 MET cc_start: 0.6852 (mmm) cc_final: 0.6543 (mmm) REVERT: A 953 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6202 (ttp80) REVERT: A 965 LEU cc_start: 0.7822 (tp) cc_final: 0.7598 (tp) REVERT: A 969 PHE cc_start: 0.7593 (m-10) cc_final: 0.7322 (m-10) REVERT: A 1072 THR cc_start: 0.5801 (m) cc_final: 0.5524 (m) REVERT: A 1107 ASP cc_start: 0.6518 (m-30) cc_final: 0.6298 (m-30) REVERT: B 113 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 276 SER cc_start: 0.8216 (m) cc_final: 0.7820 (p) REVERT: B 285 LYS cc_start: 0.7181 (mmmt) cc_final: 0.6784 (mmmt) REVERT: C 300 ILE cc_start: 0.8407 (mm) cc_final: 0.8174 (mt) REVERT: C 346 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6441 (mtp) outliers start: 40 outliers final: 17 residues processed: 254 average time/residue: 0.5709 time to fit residues: 159.8896 Evaluate side-chains 251 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 404 HIS 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 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1141 VAL 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 442 LEU Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 123 optimal weight: 0.4980 chunk 101 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 911 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.204132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.179774 restraints weight = 28313.905| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.74 r_work: 0.4119 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4126 r_free = 0.4126 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3101 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= 0.141 Angle : 0.692 25.983 19224 Z= 0.336 Chirality : 0.061 1.993 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.704 177.698 2149 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.06 % Favored : 89.88 % Rotamer: Outliers : 2.64 % Allowed : 17.09 % Favored : 80.26 % 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 aren not related in a simple way. whole: -1.25 (0.21), residues: 1611 helix: 0.48 (0.23), residues: 539 sheet: 0.11 (0.39), residues: 169 loop : -1.94 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1187 TYR 0.025 0.001 TYR B 206 PHE 0.023 0.002 PHE A 749 TRP 0.014 0.001 TRP A 607 HIS 0.008 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00314 (14047) covalent geometry : angle 0.69244 (19224) hydrogen bonds : bond 0.03483 ( 462) hydrogen bonds : angle 4.44657 ( 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 274 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.529 Fit side-chains REVERT: A 299 MET cc_start: 0.7054 (mmm) cc_final: 0.6741 (tpt) REVERT: A 465 ASP cc_start: 0.6719 (m-30) cc_final: 0.6491 (m-30) REVERT: A 486 TRP cc_start: 0.7997 (p-90) cc_final: 0.7727 (p-90) REVERT: A 544 MET cc_start: 0.6960 (mmm) cc_final: 0.6657 (mmm) REVERT: A 597 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7417 (mtt180) REVERT: A 855 VAL cc_start: 0.8261 (p) cc_final: 0.8046 (p) REVERT: A 898 ILE cc_start: 0.7532 (mm) cc_final: 0.7323 (mm) REVERT: A 953 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6294 (ttp80) REVERT: A 1111 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 276 SER cc_start: 0.8184 (m) cc_final: 0.7851 (p) REVERT: C 300 ILE cc_start: 0.8377 (mm) cc_final: 0.8143 (mt) REVERT: C 346 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6473 (mtp) REVERT: C 462 MET cc_start: 0.4126 (pp-130) cc_final: 0.3519 (pp-130) outliers start: 36 outliers final: 15 residues processed: 250 average time/residue: 0.6012 time to fit residues: 164.9986 Evaluate side-chains 244 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 556 THR 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 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 383 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET 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: 1.9990 chunk 129 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 970 ASN A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.203425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.179262 restraints weight = 24397.894| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.62 r_work: 0.4125 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3361 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= 0.141 Angle : 0.702 26.006 19224 Z= 0.338 Chirality : 0.061 1.992 2097 Planarity : 0.005 0.047 2340 Dihedral : 16.652 177.643 2149 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.24 % Favored : 89.70 % Rotamer: Outliers : 2.93 % Allowed : 17.75 % Favored : 79.31 % 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 aren not related in a simple way. whole: -1.23 (0.21), residues: 1611 helix: 0.54 (0.23), residues: 539 sheet: 0.01 (0.38), residues: 169 loop : -1.93 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1187 TYR 0.025 0.001 TYR B 206 PHE 0.020 0.001 PHE A 749 TRP 0.014 0.001 TRP A 607 HIS 0.006 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00316 (14047) covalent geometry : angle 0.70224 (19224) hydrogen bonds : bond 0.03451 ( 462) hydrogen bonds : angle 4.43486 ( 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 268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.501 Fit side-chains REVERT: A 141 LEU cc_start: 0.7475 (mm) cc_final: 0.7047 (mm) REVERT: A 245 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7157 (mp) REVERT: A 416 GLU cc_start: 0.7245 (tm-30) cc_final: 0.7006 (tp30) REVERT: A 465 ASP cc_start: 0.6777 (m-30) cc_final: 0.6529 (m-30) REVERT: A 486 TRP cc_start: 0.8067 (p-90) cc_final: 0.7767 (p-90) REVERT: A 544 MET cc_start: 0.7012 (mmm) cc_final: 0.6651 (mmm) REVERT: A 953 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6185 (ttp80) REVERT: A 969 PHE cc_start: 0.7576 (m-10) cc_final: 0.7299 (m-10) REVERT: A 1057 MET cc_start: 0.2513 (mmp) cc_final: 0.0354 (pp-130) REVERT: B 132 HIS cc_start: 0.5989 (OUTLIER) cc_final: 0.4423 (t-170) REVERT: B 276 SER cc_start: 0.8197 (m) cc_final: 0.7816 (p) REVERT: C 300 ILE cc_start: 0.8401 (mm) cc_final: 0.8173 (mt) REVERT: C 346 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6496 (mtp) REVERT: C 421 MET cc_start: 0.5962 (mmm) cc_final: 0.5703 (mpm) REVERT: C 465 MET cc_start: 0.4134 (tmm) cc_final: 0.3860 (tmm) outliers start: 40 outliers final: 14 residues processed: 247 average time/residue: 0.5055 time to fit residues: 137.8475 Evaluate side-chains 238 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 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 132 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 346 MET 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: 0.5980 chunk 115 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 117 optimal weight: 0.0010 chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.202363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.179508 restraints weight = 19970.951| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.30 r_work: 0.4138 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4144 r_free = 0.4144 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4143 r_free = 0.4143 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14047 Z= 0.147 Angle : 0.716 26.004 19224 Z= 0.345 Chirality : 0.061 1.992 2097 Planarity : 0.005 0.047 2340 Dihedral : 16.641 177.480 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.55 % Favored : 89.39 % Rotamer: Outliers : 2.49 % Allowed : 19.44 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.21), residues: 1611 helix: 0.52 (0.23), residues: 539 sheet: 0.01 (0.39), residues: 168 loop : -1.96 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1187 TYR 0.025 0.001 TYR B 206 PHE 0.020 0.002 PHE A 749 TRP 0.015 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00333 (14047) covalent geometry : angle 0.71588 (19224) hydrogen bonds : bond 0.03472 ( 462) hydrogen bonds : angle 4.45547 ( 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 265 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 109 LYS cc_start: 0.7521 (ptmt) cc_final: 0.7306 (ptmt) REVERT: A 245 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (mp) REVERT: A 299 MET cc_start: 0.7134 (mmm) cc_final: 0.6751 (tpt) REVERT: A 390 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6730 (tm-30) REVERT: A 465 ASP cc_start: 0.6760 (m-30) cc_final: 0.6511 (m-30) REVERT: A 486 TRP cc_start: 0.8101 (p-90) cc_final: 0.7856 (p-90) REVERT: A 544 MET cc_start: 0.6984 (mmm) cc_final: 0.6633 (mmm) REVERT: A 1057 MET cc_start: 0.2281 (mmp) cc_final: 0.0327 (pp-130) REVERT: A 1111 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8038 (mp) REVERT: B 132 HIS cc_start: 0.5979 (OUTLIER) cc_final: 0.4437 (t-170) REVERT: B 276 SER cc_start: 0.8191 (m) cc_final: 0.7813 (p) REVERT: B 285 LYS cc_start: 0.7242 (mmmt) cc_final: 0.5650 (mmmm) REVERT: C 300 ILE cc_start: 0.8390 (mm) cc_final: 0.8176 (mt) REVERT: C 346 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6430 (mtp) REVERT: C 349 TYR cc_start: 0.5861 (m-10) cc_final: 0.5349 (m-10) REVERT: C 462 MET cc_start: 0.4372 (pp-130) cc_final: 0.4139 (pp-130) REVERT: C 465 MET cc_start: 0.4119 (tmm) cc_final: 0.3880 (tmm) outliers start: 34 outliers final: 16 residues processed: 246 average time/residue: 0.5255 time to fit residues: 142.2352 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 SER 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 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1138 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 383 VAL Chi-restraints excluded: chain C residue 298 GLU 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: 1.9990 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 388 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.199840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.176889 restraints weight = 20678.211| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.36 r_work: 0.4104 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.43 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 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4007 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= 0.178 Angle : 0.751 25.984 19224 Z= 0.363 Chirality : 0.062 1.994 2097 Planarity : 0.005 0.049 2340 Dihedral : 16.703 177.316 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.17 % Favored : 88.76 % Rotamer: Outliers : 2.64 % Allowed : 19.59 % Favored : 77.77 % 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 aren not related in a simple way. whole: -1.40 (0.21), residues: 1611 helix: 0.32 (0.23), residues: 542 sheet: -0.03 (0.39), residues: 169 loop : -1.99 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 953 TYR 0.028 0.002 TYR B 206 PHE 0.019 0.002 PHE A 749 TRP 0.020 0.002 TRP A 607 HIS 0.007 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00408 (14047) covalent geometry : angle 0.75096 (19224) hydrogen bonds : bond 0.03753 ( 462) hydrogen bonds : angle 4.61230 ( 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 267 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 231 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7249 (mp) REVERT: A 299 MET cc_start: 0.7209 (mmm) cc_final: 0.6886 (tpt) REVERT: A 390 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: A 394 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7042 (mm-40) REVERT: A 416 GLU cc_start: 0.7226 (tm-30) cc_final: 0.7018 (tp30) REVERT: A 447 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: A 465 ASP cc_start: 0.6792 (m-30) cc_final: 0.6543 (m-30) REVERT: A 478 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6906 (ttp80) REVERT: A 486 TRP cc_start: 0.8160 (p-90) cc_final: 0.7898 (p-90) REVERT: A 544 MET cc_start: 0.6998 (mmm) cc_final: 0.6639 (mmm) REVERT: A 856 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: A 1057 MET cc_start: 0.2101 (mmp) cc_final: 0.0572 (pp-130) REVERT: A 1102 GLN cc_start: 0.7798 (mt0) cc_final: 0.7472 (mt0) REVERT: A 1111 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8112 (mp) REVERT: B 132 HIS cc_start: 0.6001 (OUTLIER) cc_final: 0.4361 (t-170) REVERT: B 276 SER cc_start: 0.8196 (m) cc_final: 0.7848 (p) REVERT: B 285 LYS cc_start: 0.7280 (mmmt) cc_final: 0.6027 (mmmt) REVERT: C 300 ILE cc_start: 0.8412 (mm) cc_final: 0.8206 (mt) REVERT: C 346 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6539 (mtp) REVERT: C 349 TYR cc_start: 0.5994 (m-10) cc_final: 0.5412 (m-10) REVERT: C 462 MET cc_start: 0.4607 (pp-130) cc_final: 0.4077 (pp-130) REVERT: C 465 MET cc_start: 0.4320 (tmm) cc_final: 0.4048 (tmm) outliers start: 36 outliers final: 19 residues processed: 247 average time/residue: 0.5417 time to fit residues: 147.1680 Evaluate side-chains 253 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 310 SER 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 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1138 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 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 C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 277 HIS A 388 ASN A 420 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.200678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.178270 restraints weight = 19445.730| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.25 r_work: 0.4122 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4127 r_free = 0.4127 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14047 Z= 0.151 Angle : 0.739 25.983 19224 Z= 0.357 Chirality : 0.062 1.992 2097 Planarity : 0.005 0.052 2340 Dihedral : 16.650 177.043 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.12 % Favored : 89.82 % Rotamer: Outliers : 2.57 % Allowed : 19.96 % 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 aren not related in a simple way. whole: -1.37 (0.21), residues: 1611 helix: 0.38 (0.23), residues: 542 sheet: -0.01 (0.39), residues: 169 loop : -2.00 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1187 TYR 0.027 0.001 TYR B 206 PHE 0.019 0.002 PHE A 749 TRP 0.017 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00341 (14047) covalent geometry : angle 0.73919 (19224) hydrogen bonds : bond 0.03531 ( 462) hydrogen bonds : angle 4.57202 ( 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 263 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.7512 (ptmt) cc_final: 0.7306 (ptmt) REVERT: A 245 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7187 (mp) REVERT: A 299 MET cc_start: 0.7114 (mmm) cc_final: 0.6833 (tpt) REVERT: A 390 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: A 394 GLN cc_start: 0.7300 (mm-40) cc_final: 0.6999 (mm110) REVERT: A 416 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6982 (tp30) REVERT: A 447 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: A 465 ASP cc_start: 0.6774 (m-30) cc_final: 0.6474 (m-30) REVERT: A 478 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6722 (ttp80) REVERT: A 486 TRP cc_start: 0.8146 (p-90) cc_final: 0.7912 (p-90) REVERT: A 616 GLU cc_start: 0.4685 (tm-30) cc_final: 0.4168 (pp20) REVERT: A 1057 MET cc_start: 0.2009 (mmp) cc_final: 0.0571 (pp-130) REVERT: A 1102 GLN cc_start: 0.7641 (mt0) cc_final: 0.7415 (mt0) REVERT: A 1111 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8042 (mp) REVERT: A 1163 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6384 (tpp) REVERT: B 132 HIS cc_start: 0.5997 (OUTLIER) cc_final: 0.4406 (t-170) REVERT: B 276 SER cc_start: 0.8200 (m) cc_final: 0.7840 (p) REVERT: B 285 LYS cc_start: 0.7254 (mmmt) cc_final: 0.6009 (mmmt) REVERT: C 300 ILE cc_start: 0.8388 (mm) cc_final: 0.8174 (mt) REVERT: C 346 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6475 (mtp) REVERT: C 349 TYR cc_start: 0.6071 (m-10) cc_final: 0.5468 (m-10) REVERT: C 462 MET cc_start: 0.4581 (pp-130) cc_final: 0.3972 (pp-130) REVERT: C 465 MET cc_start: 0.4347 (OUTLIER) cc_final: 0.4084 (tmm) outliers start: 35 outliers final: 16 residues processed: 244 average time/residue: 0.5634 time to fit residues: 151.1616 Evaluate side-chains 247 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE 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 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET 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 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 740 ASN A1202 ASN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.198660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176517 restraints weight = 19195.793| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.21 r_work: 0.4101 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3942 r_free = 0.3942 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14047 Z= 0.178 Angle : 0.769 25.974 19224 Z= 0.371 Chirality : 0.063 1.994 2097 Planarity : 0.005 0.055 2340 Dihedral : 16.689 177.023 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.05 % Favored : 88.89 % Rotamer: Outliers : 2.35 % Allowed : 20.62 % Favored : 77.04 % 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 aren not related in a simple way. whole: -1.51 (0.21), residues: 1611 helix: 0.16 (0.23), residues: 548 sheet: -0.00 (0.40), residues: 169 loop : -2.04 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 953 TYR 0.027 0.002 TYR B 206 PHE 0.019 0.002 PHE A 749 TRP 0.019 0.002 TRP A 347 HIS 0.007 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00408 (14047) covalent geometry : angle 0.76866 (19224) hydrogen bonds : bond 0.03789 ( 462) hydrogen bonds : angle 4.65962 ( 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 255 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.324 Fit side-chains REVERT: A 245 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.7280 (mp) REVERT: A 390 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: A 416 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7334 (tp30) REVERT: A 447 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7052 (pp20) REVERT: A 465 ASP cc_start: 0.7045 (m-30) cc_final: 0.6778 (m-30) REVERT: A 478 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6735 (ttp80) REVERT: A 486 TRP cc_start: 0.8229 (p-90) cc_final: 0.7960 (p-90) REVERT: A 544 MET cc_start: 0.7614 (mmm) cc_final: 0.7310 (mmm) REVERT: A 616 GLU cc_start: 0.5396 (tm-30) cc_final: 0.4622 (tm-30) REVERT: A 1057 MET cc_start: 0.2214 (mmp) cc_final: 0.0772 (pp-130) REVERT: A 1111 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 132 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.4375 (t-170) REVERT: B 276 SER cc_start: 0.8251 (m) cc_final: 0.7895 (p) REVERT: B 285 LYS cc_start: 0.7440 (mmmt) cc_final: 0.6122 (mmmt) REVERT: C 300 ILE cc_start: 0.8535 (mm) cc_final: 0.8335 (mt) REVERT: C 346 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6845 (mtp) REVERT: C 349 TYR cc_start: 0.6525 (m-10) cc_final: 0.5781 (m-10) REVERT: C 375 HIS cc_start: 0.5599 (m170) cc_final: 0.5377 (m-70) REVERT: C 462 MET cc_start: 0.4967 (pp-130) cc_final: 0.4334 (pp-130) REVERT: C 465 MET cc_start: 0.4621 (OUTLIER) cc_final: 0.4370 (tmm) outliers start: 32 outliers final: 20 residues processed: 241 average time/residue: 0.5054 time to fit residues: 134.3712 Evaluate side-chains 246 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 245 ILE 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 478 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 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 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1202 ASN 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 336 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 122 optimal weight: 0.8980 chunk 157 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 52 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 33 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 113 optimal weight: 0.0870 overall best weight: 0.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.201012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.178958 restraints weight = 19588.993| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.24 r_work: 0.4131 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4136 r_free = 0.4136 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14047 Z= 0.133 Angle : 0.741 25.958 19224 Z= 0.356 Chirality : 0.061 1.994 2097 Planarity : 0.005 0.050 2340 Dihedral : 16.605 176.677 2149 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.99 % Favored : 89.94 % Rotamer: Outliers : 1.76 % Allowed : 21.06 % Favored : 77.18 % 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 aren not related in a simple way. whole: -1.35 (0.21), residues: 1611 helix: 0.49 (0.24), residues: 533 sheet: 0.02 (0.38), residues: 180 loop : -2.05 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 953 TYR 0.024 0.001 TYR B 206 PHE 0.022 0.001 PHE A 749 TRP 0.015 0.001 TRP A1118 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00289 (14047) covalent geometry : angle 0.74088 (19224) hydrogen bonds : bond 0.03419 ( 462) hydrogen bonds : angle 4.55820 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.80 seconds wall clock time: 81 minutes 35.21 seconds (4895.21 seconds total)