Starting phenix.real_space_refine on Thu May 15 20:53:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5k_29747/05_2025/8g5k_29747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5k_29747/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5k_29747/05_2025/8g5k_29747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5k_29747/05_2025/8g5k_29747.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5k_29747/05_2025/8g5k_29747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5k_29747/05_2025/8g5k_29747.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'ASP:plan': 1, 'TYR:plan': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 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, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG: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: 8.55, per 1000 atoms: 0.63 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: 3.56 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 4.85 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: 5.15 Time building geometry restraints manager: 4.18 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.002 TRP A 607 HIS 0.011 0.001 HIS C 309 PHE 0.030 0.002 PHE A 197 TYR 0.027 0.001 TYR C 417 ARG 0.007 0.000 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.13107 ( 462) hydrogen bonds : angle 5.86470 ( 1310) covalent geometry : bond 0.00468 (14047) covalent geometry : angle 1.07339 (19224) *********************** 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 : 1.398 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: 1.1026 time to fit residues: 323.6049 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 : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.0370 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS 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 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 323 HIS B 404 ASN C 133 HIS C 422 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.213461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.191011 restraints weight = 20042.687| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 2.23 r_work: 0.4256 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14047 Z= 0.141 Angle : 0.735 26.344 19224 Z= 0.350 Chirality : 0.061 1.989 2097 Planarity : 0.005 0.064 2340 Dihedral : 16.775 177.072 2149 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.57 % Favored : 91.37 % Rotamer: Outliers : 2.42 % Allowed : 9.68 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.20), residues: 1611 helix: 0.57 (0.23), residues: 521 sheet: -0.17 (0.37), residues: 171 loop : -2.00 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.006 0.001 HIS C 133 PHE 0.023 0.002 PHE A 749 TYR 0.023 0.001 TYR B 206 ARG 0.006 0.001 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 462) hydrogen bonds : angle 4.59674 ( 1310) covalent geometry : bond 0.00311 (14047) covalent geometry : angle 0.73532 (19224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.524 Fit side-chains REVERT: A 100 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7116 (m) REVERT: A 220 TRP cc_start: 0.5139 (m100) cc_final: 0.4598 (m100) REVERT: A 434 TYR cc_start: 0.7557 (t80) cc_final: 0.7050 (t80) REVERT: A 465 ASP cc_start: 0.6907 (m-30) cc_final: 0.6679 (m-30) REVERT: A 544 MET cc_start: 0.6886 (mmm) cc_final: 0.6628 (mmm) REVERT: A 953 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6122 (mtm110) REVERT: A 1057 MET cc_start: 0.3975 (mmm) cc_final: 0.1783 (ptm) REVERT: A 1107 ASP cc_start: 0.6393 (m-30) cc_final: 0.6149 (m-30) REVERT: B 256 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7246 (tp) REVERT: B 404 ASN cc_start: 0.7489 (m-40) cc_final: 0.7256 (m-40) REVERT: B 458 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: C 300 ILE cc_start: 0.8240 (mm) cc_final: 0.7966 (mt) outliers start: 33 outliers final: 9 residues processed: 245 average time/residue: 1.1485 time to fit residues: 310.7058 Evaluate side-chains 228 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 157 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 73 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS A 404 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS C 133 HIS C 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.207974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.184698 restraints weight = 20137.549| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.32 r_work: 0.4181 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14047 Z= 0.151 Angle : 0.716 25.875 19224 Z= 0.345 Chirality : 0.062 2.000 2097 Planarity : 0.005 0.050 2340 Dihedral : 16.734 177.966 2149 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.50 % Favored : 90.44 % Rotamer: Outliers : 3.15 % Allowed : 12.69 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1611 helix: 0.48 (0.23), residues: 537 sheet: -0.14 (0.36), residues: 184 loop : -1.97 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.009 0.001 HIS A 805 PHE 0.026 0.002 PHE A 749 TYR 0.027 0.001 TYR B 206 ARG 0.010 0.001 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 462) hydrogen bonds : angle 4.47577 ( 1310) covalent geometry : bond 0.00331 (14047) covalent geometry : angle 0.71572 (19224) *********************** 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 280 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7817 (mmt-90) REVERT: A 297 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6917 (mtt) REVERT: A 416 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6871 (tp30) REVERT: A 465 ASP cc_start: 0.6906 (m-30) cc_final: 0.6622 (m-30) REVERT: A 486 TRP cc_start: 0.7926 (p-90) cc_final: 0.7660 (p-90) REVERT: A 544 MET cc_start: 0.6942 (mmm) cc_final: 0.6622 (mmm) REVERT: A 803 ASN cc_start: 0.7558 (t0) cc_final: 0.7292 (t0) REVERT: A 953 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6100 (mtm110) REVERT: A 969 PHE cc_start: 0.7469 (m-10) cc_final: 0.7228 (m-10) REVERT: B 186 LEU cc_start: 0.7700 (mp) cc_final: 0.7493 (mp) REVERT: B 260 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7319 (mt) REVERT: B 285 LYS cc_start: 0.6825 (mmmt) cc_final: 0.6577 (tptp) REVERT: B 404 ASN cc_start: 0.7761 (m-40) cc_final: 0.7520 (m110) REVERT: B 435 MET cc_start: 0.8273 (mtp) cc_final: 0.8055 (mtp) REVERT: C 300 ILE cc_start: 0.8340 (mm) cc_final: 0.8105 (mt) REVERT: C 346 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6272 (mtp) REVERT: C 382 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.4957 (mppt) REVERT: C 462 MET cc_start: 0.4011 (pp-130) cc_final: 0.3241 (pp-130) outliers start: 43 outliers final: 11 residues processed: 254 average time/residue: 1.1107 time to fit residues: 311.5025 Evaluate side-chains 250 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 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 442 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 382 LYS Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 55 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.0118 ------------------------------------------------------------------------------- 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** C 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.202307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.177131 restraints weight = 27525.148| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.82 r_work: 0.4091 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14047 Z= 0.204 Angle : 0.754 26.006 19224 Z= 0.368 Chirality : 0.063 1.994 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.849 177.687 2149 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.87 % Favored : 90.01 % Rotamer: Outliers : 3.23 % Allowed : 14.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1611 helix: 0.25 (0.22), residues: 538 sheet: -0.09 (0.37), residues: 181 loop : -2.01 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 607 HIS 0.025 0.002 HIS A 404 PHE 0.022 0.002 PHE A 749 TYR 0.028 0.002 TYR B 206 ARG 0.007 0.001 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 462) hydrogen bonds : angle 4.58542 ( 1310) covalent geometry : bond 0.00463 (14047) covalent geometry : angle 0.75367 (19224) *********************** 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 284 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.570 Fit side-chains REVERT: A 86 GLN cc_start: 0.6222 (mm-40) cc_final: 0.5645 (mm-40) REVERT: A 465 ASP cc_start: 0.6886 (m-30) cc_final: 0.6660 (m-30) REVERT: A 486 TRP cc_start: 0.8143 (p-90) cc_final: 0.7811 (p-90) REVERT: A 544 MET cc_start: 0.6921 (mmm) cc_final: 0.6583 (mmm) REVERT: A 803 ASN cc_start: 0.7571 (t0) cc_final: 0.7337 (t0) REVERT: A 898 ILE cc_start: 0.7504 (mm) cc_final: 0.7290 (mm) REVERT: A 953 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6193 (mtm110) REVERT: A 1057 MET cc_start: 0.4066 (mmm) cc_final: 0.0823 (pp-130) REVERT: A 1111 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 256 LEU cc_start: 0.7828 (tm) cc_final: 0.7569 (tp) REVERT: B 285 LYS cc_start: 0.7317 (mmmt) cc_final: 0.5751 (mmmm) REVERT: B 435 MET cc_start: 0.8427 (mtp) cc_final: 0.8194 (mtp) REVERT: C 300 ILE cc_start: 0.8447 (mm) cc_final: 0.8183 (mt) REVERT: C 346 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6564 (mtp) outliers start: 44 outliers final: 17 residues processed: 257 average time/residue: 1.1488 time to fit residues: 325.0910 Evaluate side-chains 252 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 953 ARG Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 431 LYS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain C residue 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 97 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 91 optimal weight: 0.0010 chunk 143 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN C 249 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.204848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.182063 restraints weight = 19621.386| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 2.24 r_work: 0.4161 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4174 r_free = 0.4174 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3240 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= 0.125 Angle : 0.683 25.972 19224 Z= 0.331 Chirality : 0.061 1.992 2097 Planarity : 0.005 0.046 2340 Dihedral : 16.671 177.645 2149 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.12 % Favored : 90.75 % Rotamer: Outliers : 2.93 % Allowed : 17.31 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.21), residues: 1611 helix: 0.51 (0.23), residues: 538 sheet: 0.04 (0.40), residues: 161 loop : -1.97 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 347 HIS 0.003 0.001 HIS A 805 PHE 0.020 0.001 PHE A 749 TYR 0.022 0.001 TYR B 206 ARG 0.007 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 462) hydrogen bonds : angle 4.37293 ( 1310) covalent geometry : bond 0.00273 (14047) covalent geometry : angle 0.68324 (19224) *********************** 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 265 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 1.366 Fit side-chains REVERT: A 86 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5743 (mm-40) REVERT: A 416 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6943 (tp30) REVERT: A 465 ASP cc_start: 0.6749 (m-30) cc_final: 0.6489 (m-30) REVERT: A 486 TRP cc_start: 0.8022 (p-90) cc_final: 0.7768 (p-90) REVERT: A 544 MET cc_start: 0.6913 (mmm) cc_final: 0.6578 (mmm) REVERT: A 597 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7353 (mtt180) REVERT: A 803 ASN cc_start: 0.7522 (t0) cc_final: 0.7303 (t0) REVERT: A 898 ILE cc_start: 0.7423 (mm) cc_final: 0.7194 (mm) REVERT: A 920 THR cc_start: 0.5884 (OUTLIER) cc_final: 0.5671 (m) REVERT: A 953 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.6126 (ttp80) REVERT: A 969 PHE cc_start: 0.7563 (m-10) cc_final: 0.7284 (m-10) REVERT: A 1111 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8001 (mp) REVERT: C 260 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 300 ILE cc_start: 0.8340 (mm) cc_final: 0.8086 (mt) REVERT: C 346 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6299 (mtp) REVERT: C 462 MET cc_start: 0.4167 (pp-130) cc_final: 0.3547 (pp-130) outliers start: 40 outliers final: 16 residues processed: 239 average time/residue: 1.1639 time to fit residues: 306.8886 Evaluate side-chains 232 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 920 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 331 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 260 LEU 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 50 optimal weight: 0.0970 chunk 91 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 970 ASN A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN C 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.200873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.176920 restraints weight = 23171.264| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.48 r_work: 0.4110 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4118 r_free = 0.4118 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14047 Z= 0.177 Angle : 0.735 26.012 19224 Z= 0.355 Chirality : 0.062 1.993 2097 Planarity : 0.005 0.045 2340 Dihedral : 16.720 177.722 2149 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.55 % Favored : 89.32 % Rotamer: Outliers : 2.86 % Allowed : 17.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1611 helix: 0.40 (0.23), residues: 540 sheet: 0.01 (0.40), residues: 161 loop : -1.96 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 607 HIS 0.006 0.001 HIS A 805 PHE 0.028 0.002 PHE A 749 TYR 0.027 0.002 TYR B 206 ARG 0.008 0.001 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 462) hydrogen bonds : angle 4.54101 ( 1310) covalent geometry : bond 0.00404 (14047) covalent geometry : angle 0.73510 (19224) *********************** 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 269 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 1.507 Fit side-chains REVERT: A 299 MET cc_start: 0.7171 (mmm) cc_final: 0.6847 (tpt) REVERT: A 390 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6574 (tm-30) REVERT: A 465 ASP cc_start: 0.6725 (m-30) cc_final: 0.6480 (m-30) REVERT: A 486 TRP cc_start: 0.8064 (p-90) cc_final: 0.7827 (p-90) REVERT: A 544 MET cc_start: 0.7032 (mmm) cc_final: 0.6660 (mmm) REVERT: A 803 ASN cc_start: 0.7509 (t0) cc_final: 0.7282 (t0) REVERT: A 856 GLU cc_start: 0.7614 (tp30) cc_final: 0.7370 (tp30) REVERT: A 898 ILE cc_start: 0.7465 (mm) cc_final: 0.7241 (mm) REVERT: A 953 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6269 (ttp80) REVERT: A 1057 MET cc_start: 0.2465 (mmp) cc_final: 0.0331 (pp-130) REVERT: A 1111 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 132 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.4460 (t-170) REVERT: B 256 LEU cc_start: 0.7815 (tm) cc_final: 0.7552 (tp) REVERT: C 260 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7497 (tp) REVERT: C 300 ILE cc_start: 0.8400 (mm) cc_final: 0.8152 (mt) REVERT: C 346 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6533 (mtp) REVERT: C 349 TYR cc_start: 0.5776 (m-10) cc_final: 0.5304 (m-10) outliers start: 39 outliers final: 18 residues processed: 250 average time/residue: 1.1287 time to fit residues: 312.6810 Evaluate side-chains 247 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 778 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 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 247 THR Chi-restraints excluded: chain C residue 260 LEU 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 94 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 chunk 132 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 420 HIS A1102 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.203309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.180470 restraints weight = 20023.841| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.29 r_work: 0.4147 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4156 r_free = 0.4156 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14047 Z= 0.128 Angle : 0.699 26.009 19224 Z= 0.337 Chirality : 0.061 1.991 2097 Planarity : 0.004 0.049 2340 Dihedral : 16.625 177.415 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.62 % Favored : 90.25 % Rotamer: Outliers : 2.20 % Allowed : 19.96 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1611 helix: 0.57 (0.23), residues: 539 sheet: 0.05 (0.40), residues: 154 loop : -1.91 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 607 HIS 0.005 0.001 HIS C 323 PHE 0.025 0.001 PHE A 749 TYR 0.025 0.001 TYR B 206 ARG 0.006 0.000 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 462) hydrogen bonds : angle 4.38924 ( 1310) covalent geometry : bond 0.00283 (14047) covalent geometry : angle 0.69949 (19224) *********************** 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 256 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 1.416 Fit side-chains REVERT: A 141 LEU cc_start: 0.7494 (mm) cc_final: 0.7290 (mp) REVERT: A 390 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: A 465 ASP cc_start: 0.6713 (m-30) cc_final: 0.6435 (m-30) REVERT: A 486 TRP cc_start: 0.8070 (p-90) cc_final: 0.7828 (p-90) REVERT: A 803 ASN cc_start: 0.7500 (t0) cc_final: 0.7268 (t0) REVERT: A 898 ILE cc_start: 0.7403 (mm) cc_final: 0.7184 (mm) REVERT: A 985 MET cc_start: 0.4952 (mmt) cc_final: 0.4696 (mmt) REVERT: A 1057 MET cc_start: 0.2321 (mmp) cc_final: 0.0265 (pp-130) REVERT: A 1111 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8011 (mp) REVERT: B 132 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.4389 (t-170) REVERT: B 276 SER cc_start: 0.8341 (m) cc_final: 0.8016 (p) REVERT: B 285 LYS cc_start: 0.7177 (mmmt) cc_final: 0.5977 (mmmt) REVERT: C 260 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7467 (tp) REVERT: C 346 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6382 (mtp) REVERT: C 349 TYR cc_start: 0.5804 (m-10) cc_final: 0.5301 (m-10) outliers start: 30 outliers final: 14 residues processed: 243 average time/residue: 1.1062 time to fit residues: 297.4872 Evaluate side-chains 241 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 491 ASP 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 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 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.198159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.175541 restraints weight = 19682.308| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 2.20 r_work: 0.4077 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3934 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14047 Z= 0.211 Angle : 0.775 25.976 19224 Z= 0.379 Chirality : 0.063 1.997 2097 Planarity : 0.005 0.046 2340 Dihedral : 16.782 177.425 2149 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.17 % Favored : 88.76 % Rotamer: Outliers : 2.42 % Allowed : 20.18 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1611 helix: 0.06 (0.22), residues: 557 sheet: -0.08 (0.39), residues: 180 loop : -2.00 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 607 HIS 0.007 0.001 HIS B 77 PHE 0.028 0.002 PHE A 749 TYR 0.031 0.002 TYR B 206 ARG 0.010 0.001 ARG A 597 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 462) hydrogen bonds : angle 4.66000 ( 1310) covalent geometry : bond 0.00488 (14047) covalent geometry : angle 0.77475 (19224) *********************** 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 261 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.7431 (mmm) cc_final: 0.6989 (tpt) REVERT: A 390 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 465 ASP cc_start: 0.6985 (m-30) cc_final: 0.6734 (m-30) REVERT: A 478 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6953 (ttp80) REVERT: A 486 TRP cc_start: 0.8240 (p-90) cc_final: 0.8036 (p-90) REVERT: A 544 MET cc_start: 0.7606 (mmm) cc_final: 0.7301 (mmm) REVERT: A 853 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7306 (ptp-110) REVERT: A 1057 MET cc_start: 0.2411 (mmp) cc_final: 0.0751 (pp-130) REVERT: A 1111 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 106 LEU cc_start: 0.7560 (tp) cc_final: 0.7268 (tp) REVERT: B 132 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.4619 (t-170) REVERT: B 276 SER cc_start: 0.8419 (m) cc_final: 0.8137 (p) REVERT: C 260 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7697 (tp) REVERT: C 346 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6902 (mtp) REVERT: C 349 TYR cc_start: 0.6287 (m-10) cc_final: 0.5640 (m-10) REVERT: C 462 MET cc_start: 0.5137 (pp-130) cc_final: 0.4933 (pp-130) outliers start: 33 outliers final: 18 residues processed: 246 average time/residue: 1.0799 time to fit residues: 294.6070 Evaluate side-chains 243 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU 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 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 111 optimal weight: 0.8980 chunk 156 optimal weight: 20.0000 chunk 144 optimal weight: 0.5980 chunk 161 optimal weight: 0.1980 chunk 143 optimal weight: 4.9990 chunk 155 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A1102 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.200925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.178569 restraints weight = 19367.775| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.25 r_work: 0.4129 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14047 Z= 0.135 Angle : 0.738 25.973 19224 Z= 0.354 Chirality : 0.062 1.992 2097 Planarity : 0.005 0.053 2340 Dihedral : 16.666 176.901 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.68 % Favored : 90.25 % Rotamer: Outliers : 2.20 % Allowed : 21.13 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1611 helix: 0.23 (0.23), residues: 555 sheet: -0.01 (0.40), residues: 170 loop : -1.99 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.006 0.001 HIS A 277 PHE 0.029 0.002 PHE A 273 TYR 0.026 0.001 TYR B 206 ARG 0.008 0.000 ARG A1187 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 462) hydrogen bonds : angle 4.48784 ( 1310) covalent geometry : bond 0.00301 (14047) covalent geometry : angle 0.73809 (19224) *********************** 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 251 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7385 (mmm) cc_final: 0.6864 (tpt) REVERT: A 390 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6658 (tm-30) REVERT: A 405 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 447 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: A 465 ASP cc_start: 0.6958 (m-30) cc_final: 0.6685 (m-30) REVERT: A 478 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6791 (ttp80) REVERT: A 544 MET cc_start: 0.7601 (mmm) cc_final: 0.7280 (mmm) REVERT: A 1057 MET cc_start: 0.2313 (mmp) cc_final: 0.0653 (pp-130) REVERT: A 1111 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 132 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.4393 (t-170) REVERT: B 276 SER cc_start: 0.8427 (m) cc_final: 0.8129 (p) REVERT: B 285 LYS cc_start: 0.7404 (mmmt) cc_final: 0.5844 (mtpp) REVERT: B 408 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: C 346 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.6720 (mtp) REVERT: C 349 TYR cc_start: 0.6345 (m-10) cc_final: 0.5709 (m-10) REVERT: C 462 MET cc_start: 0.4953 (pp-130) cc_final: 0.4703 (pp-130) outliers start: 30 outliers final: 14 residues processed: 235 average time/residue: 1.1397 time to fit residues: 295.1752 Evaluate side-chains 243 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.0020 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 151 optimal weight: 0.0370 overall best weight: 0.5870 ------------------------------------------------------------------------------- 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 A1102 GLN ** 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 = 0.4455 r_free = 0.4455 target = 0.199964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.177594 restraints weight = 19476.778| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.23 r_work: 0.4094 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4100 r_free = 0.4100 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4360 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= 0.154 Angle : 0.758 25.994 19224 Z= 0.362 Chirality : 0.062 1.992 2097 Planarity : 0.005 0.051 2340 Dihedral : 16.665 177.056 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.68 % Favored : 89.26 % Rotamer: Outliers : 2.13 % Allowed : 21.86 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1611 helix: 0.23 (0.23), residues: 555 sheet: -0.01 (0.40), residues: 170 loop : -2.02 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 486 HIS 0.005 0.001 HIS A 805 PHE 0.031 0.002 PHE A 273 TYR 0.027 0.001 TYR B 206 ARG 0.008 0.001 ARG A 953 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 462) hydrogen bonds : angle 4.51155 ( 1310) covalent geometry : bond 0.00350 (14047) covalent geometry : angle 0.75763 (19224) ********************** 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 254 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7330 (mmm) cc_final: 0.6853 (tpt) REVERT: A 390 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: A 405 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6967 (mt-10) REVERT: A 447 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6985 (pp20) REVERT: A 465 ASP cc_start: 0.6778 (m-30) cc_final: 0.6522 (m-30) REVERT: A 478 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6721 (ttp80) REVERT: A 544 MET cc_start: 0.7251 (mmm) cc_final: 0.6980 (mmm) REVERT: A 1057 MET cc_start: 0.2123 (mmp) cc_final: 0.0571 (pp-130) REVERT: A 1111 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 132 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.4398 (t-170) REVERT: B 256 LEU cc_start: 0.7751 (tm) cc_final: 0.7502 (tp) REVERT: B 276 SER cc_start: 0.8325 (m) cc_final: 0.8080 (p) REVERT: B 285 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6029 (mmmt) REVERT: C 346 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6504 (mtp) REVERT: C 349 TYR cc_start: 0.6030 (m-10) cc_final: 0.5440 (m-10) REVERT: C 462 MET cc_start: 0.4963 (pp-130) cc_final: 0.4519 (pp-130) outliers start: 29 outliers final: 17 residues processed: 241 average time/residue: 1.1078 time to fit residues: 295.9278 Evaluate side-chains 248 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 295 MET 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 491 ASP 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 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 285 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 95 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 0.0010 chunk 160 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 156 optimal weight: 0.0470 chunk 94 optimal weight: 0.5980 overall best weight: 0.3484 ------------------------------------------------------------------------------- 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 A1102 GLN ** B 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 375 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.201338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.179242 restraints weight = 19356.372| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.22 r_work: 0.4114 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3977 r_free = 0.3977 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14047 Z= 0.132 Angle : 0.747 25.984 19224 Z= 0.356 Chirality : 0.062 1.991 2097 Planarity : 0.005 0.053 2340 Dihedral : 16.600 176.733 2149 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.93 % Favored : 90.01 % Rotamer: Outliers : 2.13 % Allowed : 21.86 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1611 helix: 0.35 (0.23), residues: 549 sheet: -0.03 (0.40), residues: 170 loop : -2.05 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 486 HIS 0.004 0.001 HIS A 805 PHE 0.031 0.001 PHE A 273 TYR 0.026 0.001 TYR B 206 ARG 0.009 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 462) hydrogen bonds : angle 4.44059 ( 1310) covalent geometry : bond 0.00297 (14047) covalent geometry : angle 0.74708 (19224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9927.02 seconds wall clock time: 171 minutes 13.94 seconds (10273.94 seconds total)