Starting phenix.real_space_refine on Fri Jun 13 03:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5n_29750/06_2025/8g5n_29750_neut.cif" } resolution = 2.73 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= 0.000 sd= 0.014 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 38 5.49 5 S 79 5.16 5 C 9099 2.51 5 N 2536 2.21 5 O 2733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 919, 7217 Classifications: {'peptide': 919} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 61, 'TRANS': 857} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3247 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3224 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 427 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Time building chain proxies: 8.90, per 1000 atoms: 0.61 Number of scatterers: 14485 At special positions: 0 Unit cell: (105.677, 104.851, 146.131, 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 79 16.00 P 38 15.00 O 2733 8.00 N 2536 7.00 C 9099 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: 4.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 37.9% alpha, 11.4% beta 16 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 7.25 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.811A pdb=" N LYS A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.984A pdb=" N ALA A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.610A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.502A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.996A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 471 removed outlier: 3.539A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.571A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 481 " --> pdb=" O ARG A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.917A pdb=" N SER A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.784A pdb=" N GLU A 775 " --> pdb=" O PRO A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 803 WARNING: missing atoms! removed outlier: 5.065A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.520A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 982 through 987 Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.565A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.776A pdb=" N ARG A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.715A pdb=" N TYR A1221 " --> pdb=" O LEU A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 174 through 178 removed outlier: 4.207A pdb=" N THR B 177 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 removed outlier: 3.717A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 247 through 265 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 308 through 315 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 3.971A pdb=" N GLN B 397 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.979A pdb=" N LEU B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.913A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.505A pdb=" N PHE B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.338A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.077A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.548A pdb=" N LEU C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 395 through 409 removed outlier: 3.544A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 4.022A pdb=" N LEU C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 419 " --> pdb=" O GLY C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.724A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 removed outlier: 3.848A pdb=" N PHE C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.843A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 213 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 198 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 215 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.684A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1127 through 1133 removed outlier: 6.891A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.723A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.909A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.350A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.977A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.538A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3790 1.33 - 1.46: 3172 1.46 - 1.58: 7760 1.58 - 1.70: 77 1.70 - 1.82: 125 Bond restraints: 14924 Sorted by residual: bond pdb=" C3' G R 20 " pdb=" C2' G R 20 " ideal model delta sigma weight residual 1.525 1.622 -0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" C3' C R 16 " pdb=" C2' C R 16 " ideal model delta sigma weight residual 1.523 1.450 0.073 1.50e-02 4.44e+03 2.34e+01 bond pdb=" CG PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 1.503 1.382 0.121 3.40e-02 8.65e+02 1.27e+01 bond pdb=" N VAL A 229 " pdb=" CA VAL A 229 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N ILE A 342 " pdb=" CA ILE A 342 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 14919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 20029 3.34 - 6.69: 343 6.69 - 10.03: 36 10.03 - 13.38: 8 13.38 - 16.72: 1 Bond angle restraints: 20417 Sorted by residual: angle pdb=" CA PRO A 772 " pdb=" N PRO A 772 " pdb=" CD PRO A 772 " ideal model delta sigma weight residual 112.00 95.28 16.72 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C3' G R 21 " pdb=" O3' G R 21 " pdb=" P G R 22 " ideal model delta sigma weight residual 120.20 107.20 13.00 1.50e+00 4.44e-01 7.51e+01 angle pdb=" C3' U R 9 " pdb=" O3' U R 9 " pdb=" P G R 10 " ideal model delta sigma weight residual 120.20 107.30 12.90 1.50e+00 4.44e-01 7.39e+01 angle pdb=" C3' DT T 9 " pdb=" O3' DT T 9 " pdb=" P DC T 10 " ideal model delta sigma weight residual 120.20 108.61 11.59 1.50e+00 4.44e-01 5.97e+01 angle pdb=" C3' C R 18 " pdb=" O3' C R 18 " pdb=" P G R 19 " ideal model delta sigma weight residual 120.20 108.68 11.52 1.50e+00 4.44e-01 5.89e+01 ... (remaining 20412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7625 17.89 - 35.78: 867 35.78 - 53.66: 278 53.66 - 71.55: 91 71.55 - 89.44: 20 Dihedral angle restraints: 8881 sinusoidal: 3881 harmonic: 5000 Sorted by residual: dihedral pdb=" CD ARG C 325 " pdb=" NE ARG C 325 " pdb=" CZ ARG C 325 " pdb=" NH1 ARG C 325 " ideal model delta sinusoidal sigma weight residual 0.00 -64.03 64.03 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" C5' G R 20 " pdb=" C4' G R 20 " pdb=" C3' G R 20 " pdb=" O3' G R 20 " ideal model delta sinusoidal sigma weight residual 147.00 103.33 43.67 1 8.00e+00 1.56e-02 4.15e+01 dihedral pdb=" CD ARG C 344 " pdb=" NE ARG C 344 " pdb=" CZ ARG C 344 " pdb=" NH1 ARG C 344 " ideal model delta sinusoidal sigma weight residual 0.00 48.96 -48.96 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 8878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2141 0.127 - 0.255: 55 0.255 - 0.382: 2 0.382 - 0.510: 29 0.510 - 0.637: 8 Chirality restraints: 2235 Sorted by residual: chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " 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 G R 6 " pdb=" OP1 G R 6 " pdb=" OP2 G R 6 " pdb=" O5' G R 6 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" P DA T 6 " pdb=" OP1 DA T 6 " pdb=" OP2 DA T 6 " pdb=" O5' DA T 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.61e+00 ... (remaining 2232 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 325 " 0.988 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG C 325 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG C 325 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 325 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 325 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 344 " -0.815 9.50e-02 1.11e+02 3.66e-01 8.12e+01 pdb=" NE ARG C 344 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG C 344 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 344 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 344 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 597 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.66e+01 pdb=" NE ARG A 597 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 597 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 597 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 597 " 0.020 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 78 2.48 - 3.08: 10403 3.08 - 3.69: 22516 3.69 - 4.29: 31284 4.29 - 4.90: 51146 Nonbonded interactions: 115427 Sorted by model distance: nonbonded pdb=" OG SER A 237 " pdb=" OG SER A 240 " model vdw 1.871 3.040 nonbonded pdb=" O TYR A 282 " pdb=" OH TYR A 434 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.113 3.040 nonbonded pdb=" O THR A 210 " pdb=" OG SER A 225 " model vdw 2.119 3.040 nonbonded pdb=" O CYS A 224 " pdb=" OG SER A 225 " model vdw 2.123 3.040 ... (remaining 115422 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 66 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 146 or (resid 147 and (name N o \ r name CA or name C or name O or name CB )) or resid 148 through 170 or (resid 1 \ 71 through 176 and (name N or name CA or name C or name O or name CB )) or resid \ 177 through 222 or (resid 223 and (name N or name CA or name C or name O or nam \ e CB )) or resid 224 or (resid 225 and (name N or name CA or name C or name O or \ name CB )) or resid 226 through 283 or (resid 284 and (name N or name CA or nam \ e C or name O or name CB )) or resid 285 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 66 or (resid 67 through 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 145 o \ r (resid 146 through 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 160 or resid 170 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.250 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 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 : 0.006 0.129 14924 Z= 0.347 Angle : 1.004 16.720 20417 Z= 0.601 Chirality : 0.079 0.637 2235 Planarity : 0.016 0.443 2486 Dihedral : 17.819 89.437 5655 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.85 % Allowed : 24.35 % Favored : 73.80 % 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: -0.17 (0.21), residues: 1712 helix: 1.43 (0.23), residues: 588 sheet: 1.07 (0.36), residues: 215 loop : -1.54 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 255 HIS 0.005 0.001 HIS C 258 PHE 0.025 0.001 PHE A 539 TYR 0.010 0.001 TYR C 315 ARG 0.007 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.14517 ( 560) hydrogen bonds : angle 6.88705 ( 1524) covalent geometry : bond 0.00594 (14924) covalent geometry : angle 1.00447 (20417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.7260 (mmm) cc_final: 0.6974 (mmm) REVERT: B 465 MET cc_start: 0.7255 (mmm) cc_final: 0.7000 (mmm) outliers start: 27 outliers final: 12 residues processed: 236 average time/residue: 1.0623 time to fit residues: 281.8722 Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 GLN A 879 GLN A 976 GLN A1214 GLN B 158 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS C 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.187756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.140218 restraints weight = 26802.618| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.71 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14924 Z= 0.173 Angle : 0.710 11.235 20417 Z= 0.355 Chirality : 0.045 0.282 2235 Planarity : 0.006 0.068 2486 Dihedral : 15.382 88.476 2397 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.05 % Allowed : 22.29 % Favored : 73.66 % 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: -0.31 (0.21), residues: 1712 helix: 1.30 (0.22), residues: 606 sheet: 1.09 (0.37), residues: 209 loop : -1.69 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 607 HIS 0.004 0.001 HIS A 754 PHE 0.019 0.002 PHE A 610 TYR 0.011 0.002 TYR A1166 ARG 0.007 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 560) hydrogen bonds : angle 4.41757 ( 1524) covalent geometry : bond 0.00394 (14924) covalent geometry : angle 0.71007 (20417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.7605 (tpp) cc_final: 0.7371 (tpp) REVERT: A 544 MET cc_start: 0.6919 (mpp) cc_final: 0.6637 (mpp) REVERT: A 594 LEU cc_start: 0.6511 (mt) cc_final: 0.6210 (mp) REVERT: A 597 ARG cc_start: 0.8097 (tmm160) cc_final: 0.7688 (ttp80) REVERT: A 821 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5454 (mm) REVERT: A 1167 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8548 (mptp) REVERT: A 1206 MET cc_start: 0.2217 (OUTLIER) cc_final: 0.1884 (mmt) REVERT: B 206 TYR cc_start: 0.6584 (p90) cc_final: 0.6318 (p90) REVERT: B 241 TRP cc_start: 0.7025 (t-100) cc_final: 0.6722 (t-100) REVERT: B 405 GLU cc_start: 0.8101 (tp30) cc_final: 0.7835 (tp30) REVERT: B 465 MET cc_start: 0.6839 (mmm) cc_final: 0.6418 (mmm) REVERT: B 475 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 462 MET cc_start: 0.7710 (pp-130) cc_final: 0.7483 (ppp) outliers start: 59 outliers final: 23 residues processed: 242 average time/residue: 0.9970 time to fit residues: 272.7518 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 6 optimal weight: 4.9990 chunk 60 optimal weight: 0.0170 chunk 154 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 147 optimal weight: 0.0000 chunk 4 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 2.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 440 ASN A 740 ASN A 843 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 133 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.182768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.134312 restraints weight = 26734.748| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 4.32 r_work: 0.3809 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14924 Z= 0.233 Angle : 0.726 11.583 20417 Z= 0.368 Chirality : 0.046 0.230 2235 Planarity : 0.006 0.074 2486 Dihedral : 15.173 86.305 2384 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 5.62 % Allowed : 22.29 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.78 (0.20), residues: 1712 helix: 0.75 (0.21), residues: 620 sheet: 0.86 (0.37), residues: 203 loop : -1.88 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 607 HIS 0.009 0.001 HIS A 613 PHE 0.026 0.002 PHE A 610 TYR 0.019 0.002 TYR B 315 ARG 0.005 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 560) hydrogen bonds : angle 4.58696 ( 1524) covalent geometry : bond 0.00532 (14924) covalent geometry : angle 0.72556 (20417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 184 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.7779 (tpp) cc_final: 0.7460 (tpp) REVERT: A 544 MET cc_start: 0.7163 (mpp) cc_final: 0.6763 (mpt) REVERT: A 585 TRP cc_start: 0.6780 (t-100) cc_final: 0.6236 (t-100) REVERT: A 594 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6222 (mt) REVERT: A 597 ARG cc_start: 0.8520 (tmm160) cc_final: 0.8047 (ttp80) REVERT: A 821 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5763 (mm) REVERT: A 910 MET cc_start: 0.6954 (mpt) cc_final: 0.6498 (mpt) REVERT: A 967 MET cc_start: 0.5715 (mmt) cc_final: 0.5440 (mmt) REVERT: A 1093 MET cc_start: 0.7429 (pmt) cc_final: 0.7167 (pmm) REVERT: A 1167 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8725 (mptp) REVERT: B 180 LYS cc_start: 0.6424 (tttt) cc_final: 0.6176 (tmtt) REVERT: B 257 ARG cc_start: 0.9017 (ttm-80) cc_final: 0.8365 (ttm110) REVERT: B 405 GLU cc_start: 0.8386 (tp30) cc_final: 0.8010 (tp30) REVERT: B 427 GLN cc_start: 0.9279 (tt0) cc_final: 0.8878 (pt0) REVERT: B 465 MET cc_start: 0.6578 (mmm) cc_final: 0.6234 (mmm) REVERT: C 108 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7300 (tptp) REVERT: C 301 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7863 (tm-30) REVERT: C 462 MET cc_start: 0.7542 (pp-130) cc_final: 0.7323 (ppp) outliers start: 82 outliers final: 39 residues processed: 242 average time/residue: 1.0481 time to fit residues: 285.7467 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.185854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137749 restraints weight = 26610.646| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 4.36 r_work: 0.3854 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14924 Z= 0.140 Angle : 0.679 11.353 20417 Z= 0.335 Chirality : 0.044 0.205 2235 Planarity : 0.005 0.065 2486 Dihedral : 15.010 86.557 2384 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.39 % Allowed : 24.76 % Favored : 70.85 % 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: -0.56 (0.21), residues: 1712 helix: 1.00 (0.22), residues: 613 sheet: 0.93 (0.36), residues: 212 loop : -1.79 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 607 HIS 0.004 0.001 HIS A 277 PHE 0.028 0.001 PHE A 610 TYR 0.025 0.001 TYR B 206 ARG 0.006 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 560) hydrogen bonds : angle 4.26475 ( 1524) covalent geometry : bond 0.00315 (14924) covalent geometry : angle 0.67937 (20417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 200 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.7873 (tpp) cc_final: 0.7615 (tpp) REVERT: A 544 MET cc_start: 0.7175 (mpp) cc_final: 0.6816 (mpt) REVERT: A 585 TRP cc_start: 0.6788 (t-100) cc_final: 0.6243 (t-100) REVERT: A 594 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6048 (mt) REVERT: A 597 ARG cc_start: 0.8454 (tmm160) cc_final: 0.8010 (tmm-80) REVERT: A 910 MET cc_start: 0.6803 (mpt) cc_final: 0.6447 (mpt) REVERT: A 937 THR cc_start: 0.8362 (p) cc_final: 0.8125 (p) REVERT: A 967 MET cc_start: 0.5707 (mmt) cc_final: 0.5405 (mmt) REVERT: A 972 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7914 (mtm110) REVERT: A 1093 MET cc_start: 0.7374 (pmt) cc_final: 0.7129 (pmm) REVERT: A 1206 MET cc_start: 0.2892 (OUTLIER) cc_final: 0.2295 (mmt) REVERT: A 1209 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7419 (mtm180) REVERT: B 134 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7710 (mmtm) REVERT: B 180 LYS cc_start: 0.6206 (tttt) cc_final: 0.5844 (tmtt) REVERT: B 257 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8379 (ttm110) REVERT: B 405 GLU cc_start: 0.8403 (tp30) cc_final: 0.7987 (tp30) REVERT: B 427 GLN cc_start: 0.9225 (tt0) cc_final: 0.8871 (pt0) REVERT: B 465 MET cc_start: 0.6636 (mmm) cc_final: 0.6238 (mmm) REVERT: C 301 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7774 (tp30) REVERT: C 406 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8629 (tt) REVERT: C 462 MET cc_start: 0.7505 (pp-130) cc_final: 0.7267 (ppp) outliers start: 64 outliers final: 31 residues processed: 242 average time/residue: 1.0287 time to fit residues: 279.5353 Evaluate side-chains 215 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1209 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 46 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.0030 chunk 71 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.186214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.137875 restraints weight = 26916.436| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.44 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14924 Z= 0.136 Angle : 0.673 11.246 20417 Z= 0.332 Chirality : 0.043 0.202 2235 Planarity : 0.005 0.062 2486 Dihedral : 14.890 86.337 2384 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.39 % Allowed : 24.76 % Favored : 70.85 % 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: -0.55 (0.21), residues: 1712 helix: 1.05 (0.22), residues: 612 sheet: 0.93 (0.36), residues: 214 loop : -1.83 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 607 HIS 0.004 0.001 HIS A 613 PHE 0.035 0.001 PHE A 610 TYR 0.017 0.001 TYR A1108 ARG 0.004 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 560) hydrogen bonds : angle 4.22524 ( 1524) covalent geometry : bond 0.00305 (14924) covalent geometry : angle 0.67268 (20417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.7937 (tpp) cc_final: 0.7726 (tpp) REVERT: A 544 MET cc_start: 0.7302 (mpp) cc_final: 0.7036 (mpt) REVERT: A 585 TRP cc_start: 0.6607 (t-100) cc_final: 0.6109 (t-100) REVERT: A 594 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5950 (mt) REVERT: A 597 ARG cc_start: 0.8343 (tmm160) cc_final: 0.7938 (tmm-80) REVERT: A 821 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5370 (mm) REVERT: A 910 MET cc_start: 0.6821 (mpt) cc_final: 0.6545 (mpt) REVERT: A 967 MET cc_start: 0.5784 (mmt) cc_final: 0.5453 (mmt) REVERT: A 972 ARG cc_start: 0.8090 (mtm110) cc_final: 0.6843 (ptt-90) REVERT: A 1093 MET cc_start: 0.7214 (pmt) cc_final: 0.6977 (pmm) REVERT: A 1206 MET cc_start: 0.2152 (OUTLIER) cc_final: 0.1770 (mmt) REVERT: B 180 LYS cc_start: 0.6573 (tttt) cc_final: 0.6192 (tmtt) REVERT: B 257 ARG cc_start: 0.8949 (ttm-80) cc_final: 0.8340 (ttm110) REVERT: B 308 ASP cc_start: 0.9174 (t0) cc_final: 0.8371 (m-30) REVERT: B 405 GLU cc_start: 0.8203 (tp30) cc_final: 0.7782 (tp30) REVERT: B 465 MET cc_start: 0.6805 (mmm) cc_final: 0.6364 (mmm) outliers start: 64 outliers final: 35 residues processed: 228 average time/residue: 1.0500 time to fit residues: 269.6776 Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 39 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.185847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.138008 restraints weight = 26813.290| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 4.38 r_work: 0.3869 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14924 Z= 0.136 Angle : 0.681 11.056 20417 Z= 0.333 Chirality : 0.043 0.195 2235 Planarity : 0.005 0.060 2486 Dihedral : 14.758 85.960 2384 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.53 % Allowed : 24.97 % Favored : 70.51 % 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: -0.53 (0.21), residues: 1712 helix: 1.06 (0.22), residues: 612 sheet: 1.02 (0.36), residues: 214 loop : -1.83 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 607 HIS 0.004 0.001 HIS A 277 PHE 0.039 0.001 PHE A 610 TYR 0.026 0.001 TYR B 206 ARG 0.004 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 560) hydrogen bonds : angle 4.20312 ( 1524) covalent geometry : bond 0.00309 (14924) covalent geometry : angle 0.68148 (20417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 190 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 MET cc_start: 0.7905 (tpp) cc_final: 0.7669 (tpp) REVERT: A 544 MET cc_start: 0.7355 (mpp) cc_final: 0.7146 (mpt) REVERT: A 585 TRP cc_start: 0.6725 (t-100) cc_final: 0.6285 (t-100) REVERT: A 594 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6053 (mt) REVERT: A 597 ARG cc_start: 0.8454 (tmm160) cc_final: 0.8006 (tmm-80) REVERT: A 616 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: A 821 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5510 (mm) REVERT: A 967 MET cc_start: 0.5763 (mmt) cc_final: 0.5450 (mmt) REVERT: A 972 ARG cc_start: 0.8140 (mtm110) cc_final: 0.6818 (ptt-90) REVERT: A 1093 MET cc_start: 0.7312 (pmt) cc_final: 0.7051 (pmm) REVERT: A 1163 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7271 (tpt) REVERT: A 1206 MET cc_start: 0.2777 (OUTLIER) cc_final: 0.2222 (mmt) REVERT: B 180 LYS cc_start: 0.6176 (tttt) cc_final: 0.5959 (tmtt) REVERT: B 257 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8357 (ttm110) REVERT: B 405 GLU cc_start: 0.8395 (tp30) cc_final: 0.7970 (tp30) REVERT: B 419 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8141 (tp30) REVERT: B 465 MET cc_start: 0.6764 (mmm) cc_final: 0.6348 (mmm) REVERT: C 72 ILE cc_start: 0.6299 (pp) cc_final: 0.6094 (pp) REVERT: C 301 GLU cc_start: 0.7839 (tp30) cc_final: 0.7328 (tm-30) outliers start: 66 outliers final: 37 residues processed: 232 average time/residue: 1.0087 time to fit residues: 264.3402 Evaluate side-chains 218 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 162 optimal weight: 0.0170 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.188651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.140904 restraints weight = 27079.374| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 4.51 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14924 Z= 0.127 Angle : 0.700 11.021 20417 Z= 0.339 Chirality : 0.043 0.205 2235 Planarity : 0.004 0.057 2486 Dihedral : 14.618 85.464 2384 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 3.77 % Allowed : 26.34 % Favored : 69.89 % 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: -0.47 (0.21), residues: 1712 helix: 1.08 (0.22), residues: 611 sheet: 1.18 (0.37), residues: 207 loop : -1.78 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 345 HIS 0.004 0.001 HIS C 313 PHE 0.031 0.001 PHE A 610 TYR 0.025 0.001 TYR B 206 ARG 0.004 0.000 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 560) hydrogen bonds : angle 4.15647 ( 1524) covalent geometry : bond 0.00284 (14924) covalent geometry : angle 0.70005 (20417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 GLU cc_start: 0.8524 (mp0) cc_final: 0.8179 (mp0) REVERT: A 585 TRP cc_start: 0.6526 (t-100) cc_final: 0.5999 (t-100) REVERT: A 594 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5762 (mt) REVERT: A 597 ARG cc_start: 0.8269 (tmm160) cc_final: 0.7850 (tmm-80) REVERT: A 821 LEU cc_start: 0.5592 (OUTLIER) cc_final: 0.5341 (mm) REVERT: A 967 MET cc_start: 0.5888 (mmt) cc_final: 0.5496 (mmt) REVERT: A 972 ARG cc_start: 0.8086 (mtm110) cc_final: 0.6826 (ptp90) REVERT: A 1093 MET cc_start: 0.7258 (pmt) cc_final: 0.6976 (pmm) REVERT: A 1206 MET cc_start: 0.1949 (OUTLIER) cc_final: 0.1650 (mtt) REVERT: B 257 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8312 (ttm110) REVERT: B 308 ASP cc_start: 0.9079 (t0) cc_final: 0.8266 (m-30) REVERT: B 405 GLU cc_start: 0.8221 (tp30) cc_final: 0.7789 (tp30) REVERT: B 465 MET cc_start: 0.6996 (mmm) cc_final: 0.6543 (mmm) REVERT: C 301 GLU cc_start: 0.7848 (tp30) cc_final: 0.7463 (tm-30) REVERT: C 347 LEU cc_start: 0.8601 (tt) cc_final: 0.8393 (mt) outliers start: 55 outliers final: 32 residues processed: 232 average time/residue: 1.1774 time to fit residues: 309.2003 Evaluate side-chains 219 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 12 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.186575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.137929 restraints weight = 26784.469| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 4.53 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14924 Z= 0.149 Angle : 0.718 11.497 20417 Z= 0.349 Chirality : 0.044 0.247 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.629 85.006 2384 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.94 % Favored : 92.00 % Rotamer: Outliers : 3.77 % Allowed : 27.43 % Favored : 68.79 % 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: -0.58 (0.21), residues: 1712 helix: 1.05 (0.22), residues: 614 sheet: 1.03 (0.36), residues: 215 loop : -1.90 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 607 HIS 0.004 0.001 HIS B 77 PHE 0.031 0.002 PHE B 219 TYR 0.017 0.001 TYR A 178 ARG 0.009 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 560) hydrogen bonds : angle 4.25310 ( 1524) covalent geometry : bond 0.00340 (14924) covalent geometry : angle 0.71809 (20417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8266 (ttp80) REVERT: A 293 ASP cc_start: 0.8300 (t70) cc_final: 0.8074 (t0) REVERT: A 537 GLU cc_start: 0.8579 (mp0) cc_final: 0.8227 (mp0) REVERT: A 544 MET cc_start: 0.6854 (mpt) cc_final: 0.6401 (mpp) REVERT: A 585 TRP cc_start: 0.6495 (t-100) cc_final: 0.6091 (t-100) REVERT: A 594 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5825 (mt) REVERT: A 597 ARG cc_start: 0.8305 (tmm160) cc_final: 0.7846 (tmm-80) REVERT: A 821 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5276 (mm) REVERT: A 937 THR cc_start: 0.8280 (t) cc_final: 0.7851 (p) REVERT: A 967 MET cc_start: 0.5897 (mmt) cc_final: 0.5534 (mmt) REVERT: A 972 ARG cc_start: 0.8079 (mtm110) cc_final: 0.6989 (ptt-90) REVERT: A 1093 MET cc_start: 0.7235 (pmt) cc_final: 0.6949 (pmm) REVERT: A 1163 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7018 (tpt) REVERT: B 73 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 134 LYS cc_start: 0.7709 (mmpt) cc_final: 0.7481 (mmtm) REVERT: B 206 TYR cc_start: 0.6200 (p90) cc_final: 0.5960 (p90) REVERT: B 257 ARG cc_start: 0.8943 (ttm-80) cc_final: 0.8327 (ttm110) REVERT: B 308 ASP cc_start: 0.9122 (t0) cc_final: 0.8281 (m-30) REVERT: B 405 GLU cc_start: 0.8268 (tp30) cc_final: 0.7828 (tp30) REVERT: B 419 GLU cc_start: 0.8518 (tp30) cc_final: 0.8240 (tm-30) REVERT: B 465 MET cc_start: 0.6964 (mmm) cc_final: 0.6578 (mmm) REVERT: C 301 GLU cc_start: 0.7833 (tp30) cc_final: 0.7484 (tm-30) outliers start: 55 outliers final: 33 residues processed: 223 average time/residue: 1.0527 time to fit residues: 263.9474 Evaluate side-chains 219 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 133 HIS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 148 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 131 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.138900 restraints weight = 26816.970| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 4.50 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14924 Z= 0.137 Angle : 0.729 11.123 20417 Z= 0.355 Chirality : 0.044 0.217 2235 Planarity : 0.005 0.058 2486 Dihedral : 14.556 84.508 2383 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.06 % Favored : 91.88 % Rotamer: Outliers : 3.43 % Allowed : 27.91 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.21), residues: 1712 helix: 1.12 (0.22), residues: 607 sheet: 1.17 (0.37), residues: 207 loop : -1.91 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 345 HIS 0.005 0.001 HIS A 613 PHE 0.036 0.001 PHE A 389 TYR 0.017 0.001 TYR A 178 ARG 0.010 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 560) hydrogen bonds : angle 4.27070 ( 1524) covalent geometry : bond 0.00311 (14924) covalent geometry : angle 0.72892 (20417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8305 (ttp80) REVERT: A 285 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: A 537 GLU cc_start: 0.8582 (mp0) cc_final: 0.8214 (mp0) REVERT: A 544 MET cc_start: 0.6776 (mpt) cc_final: 0.6483 (mpp) REVERT: A 585 TRP cc_start: 0.6490 (t-100) cc_final: 0.6084 (t-100) REVERT: A 594 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5766 (mt) REVERT: A 597 ARG cc_start: 0.8292 (tmm160) cc_final: 0.7841 (tmm-80) REVERT: A 821 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5293 (mm) REVERT: A 967 MET cc_start: 0.5891 (mmt) cc_final: 0.5540 (mmt) REVERT: A 972 ARG cc_start: 0.8093 (mtm110) cc_final: 0.6873 (ptt-90) REVERT: A 1093 MET cc_start: 0.7218 (pmt) cc_final: 0.6931 (pmm) REVERT: A 1163 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7031 (tpt) REVERT: B 73 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 257 ARG cc_start: 0.8933 (ttm-80) cc_final: 0.8322 (ttm110) REVERT: B 308 ASP cc_start: 0.9103 (t0) cc_final: 0.8294 (m-30) REVERT: B 405 GLU cc_start: 0.8257 (tp30) cc_final: 0.7812 (tp30) REVERT: B 419 GLU cc_start: 0.8367 (tp30) cc_final: 0.8093 (tm-30) REVERT: B 465 MET cc_start: 0.7005 (mmm) cc_final: 0.6612 (mmm) REVERT: C 301 GLU cc_start: 0.7855 (tp30) cc_final: 0.7519 (tm-30) outliers start: 50 outliers final: 34 residues processed: 222 average time/residue: 1.0583 time to fit residues: 264.7602 Evaluate side-chains 222 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 73 CYS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS ** C 210 GLN ** 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 = 0.4615 r_free = 0.4615 target = 0.185131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.136955 restraints weight = 26961.226| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 4.45 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14924 Z= 0.164 Angle : 0.746 11.413 20417 Z= 0.368 Chirality : 0.045 0.233 2235 Planarity : 0.005 0.060 2486 Dihedral : 14.571 84.110 2383 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer: Outliers : 3.09 % Allowed : 28.46 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.64 (0.21), residues: 1712 helix: 1.06 (0.22), residues: 608 sheet: 1.01 (0.36), residues: 215 loop : -1.97 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 345 HIS 0.006 0.001 HIS A 613 PHE 0.039 0.002 PHE A 389 TYR 0.025 0.001 TYR B 206 ARG 0.010 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 560) hydrogen bonds : angle 4.34188 ( 1524) covalent geometry : bond 0.00378 (14924) covalent geometry : angle 0.74624 (20417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8323 (ttp80) REVERT: A 285 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: A 293 ASP cc_start: 0.8258 (t70) cc_final: 0.8056 (t0) REVERT: A 297 MET cc_start: 0.8376 (mpp) cc_final: 0.8036 (mtt) REVERT: A 537 GLU cc_start: 0.8584 (mp0) cc_final: 0.8217 (mp0) REVERT: A 544 MET cc_start: 0.6936 (mpt) cc_final: 0.6642 (mpp) REVERT: A 594 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5781 (mt) REVERT: A 597 ARG cc_start: 0.8356 (tmm160) cc_final: 0.7896 (tmm-80) REVERT: A 821 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5323 (mm) REVERT: A 972 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7276 (ptt-90) REVERT: A 1093 MET cc_start: 0.7213 (pmt) cc_final: 0.6922 (pmm) REVERT: A 1163 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7048 (tpt) REVERT: B 257 ARG cc_start: 0.8941 (ttm-80) cc_final: 0.8326 (ttm110) REVERT: B 308 ASP cc_start: 0.9113 (t0) cc_final: 0.8288 (m-30) REVERT: B 405 GLU cc_start: 0.8291 (tp30) cc_final: 0.7728 (tp30) REVERT: B 419 GLU cc_start: 0.8119 (tp30) cc_final: 0.7836 (pp20) REVERT: B 427 GLN cc_start: 0.9027 (tt0) cc_final: 0.8734 (pt0) REVERT: B 463 LYS cc_start: 0.6620 (pptt) cc_final: 0.6312 (pptt) REVERT: B 465 MET cc_start: 0.6976 (mmm) cc_final: 0.6593 (mmm) outliers start: 45 outliers final: 34 residues processed: 215 average time/residue: 1.0672 time to fit residues: 257.6168 Evaluate side-chains 220 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.187055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.139121 restraints weight = 26950.707| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.45 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14924 Z= 0.138 Angle : 0.757 11.409 20417 Z= 0.368 Chirality : 0.044 0.217 2235 Planarity : 0.005 0.070 2486 Dihedral : 14.535 83.673 2383 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.24 % Favored : 91.71 % Rotamer: Outliers : 3.16 % Allowed : 28.67 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.63 (0.21), residues: 1712 helix: 0.97 (0.22), residues: 611 sheet: 1.12 (0.36), residues: 208 loop : -1.90 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 345 HIS 0.008 0.001 HIS A 613 PHE 0.034 0.001 PHE A 389 TYR 0.025 0.001 TYR B 206 ARG 0.009 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 560) hydrogen bonds : angle 4.29550 ( 1524) covalent geometry : bond 0.00312 (14924) covalent geometry : angle 0.75694 (20417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12143.79 seconds wall clock time: 208 minutes 57.40 seconds (12537.40 seconds total)