Starting phenix.real_space_refine on Sun Nov 17 15:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5i_29745/11_2024/8g5i_29745.cif" } resolution = 2.75 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 80 5.16 5 C 8859 2.51 5 N 2480 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7430 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 63, 'TRANS': 877} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2986 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 355} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2890 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 395 Chain: "T" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA P 27 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 27 " occ=0.50 Time building chain proxies: 8.88, per 1000 atoms: 0.63 Number of scatterers: 14084 At special positions: 0 Unit cell: (94.164, 106.554, 141.246, 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 80 16.00 P 38 15.00 O 2627 8.00 N 2480 7.00 C 8859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 41.6% alpha, 11.3% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 removed outlier: 4.277A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Proline residue: A 149 - end of helix removed outlier: 3.503A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.875A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.501A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) 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: 4.000A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.599A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.414A pdb=" N ASP A 487 " --> pdb=" O TRP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 538 removed outlier: 3.767A pdb=" N GLU A 538 " --> pdb=" O GLU A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 538' Processing helix chain 'A' and resid 539 through 556 removed outlier: 3.676A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.623A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.656A pdb=" N MET A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.875A pdb=" N ASN A 758 " --> pdb=" O LYS A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.715A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.548A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 3.527A pdb=" N LEU A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.896A pdb=" N LEU A 965 " --> pdb=" O PHE A 961 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 966 " --> pdb=" O ALA A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.133A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.667A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 removed outlier: 3.729A pdb=" N ARG A1161 " --> pdb=" O ASN A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 removed outlier: 4.113A pdb=" N ILE A1220 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.552A pdb=" N ALA B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) 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 removed outlier: 3.547A pdb=" N LEU B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.637A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.570A pdb=" N SER B 424 " --> pdb=" O MET B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.147A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 4.184A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 87 removed outlier: 4.364A pdb=" N SER C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 184 through 191 removed outlier: 4.213A pdb=" N GLY C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 191 " --> pdb=" O HIS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.717A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.233A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 393 through 409 removed outlier: 3.643A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 470 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.868A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.785A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 605 through 606 Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133 removed outlier: 3.641A pdb=" N ARG A1138 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A1133 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1137 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.127A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.068A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 382 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 127 removed outlier: 6.269A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.111A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4439 1.34 - 1.46: 2856 1.46 - 1.58: 7023 1.58 - 1.70: 73 1.70 - 1.82: 125 Bond restraints: 14516 Sorted by residual: bond pdb=" O3' DG P 26 " pdb=" P A DA P 27 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.50e-02 4.44e+03 3.07e+01 bond pdb=" N ARG A 852 " pdb=" CA ARG A 852 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.68e+00 bond pdb=" N LEU A 605 " pdb=" CA LEU A 605 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" N ARG A 853 " pdb=" CA ARG A 853 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.14e+00 bond pdb=" N VAL A1101 " pdb=" CA VAL A1101 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.94e+00 ... (remaining 14511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 19454 2.79 - 5.57: 353 5.57 - 8.36: 22 8.36 - 11.14: 2 11.14 - 13.93: 1 Bond angle restraints: 19832 Sorted by residual: angle pdb=" N PRO A 560 " pdb=" CA PRO A 560 " pdb=" CB PRO A 560 " ideal model delta sigma weight residual 103.25 111.48 -8.23 1.05e+00 9.07e-01 6.15e+01 angle pdb=" N PRO A 625 " pdb=" CA PRO A 625 " pdb=" CB PRO A 625 " ideal model delta sigma weight residual 103.33 110.42 -7.09 9.30e-01 1.16e+00 5.81e+01 angle pdb=" N PRO A 250 " pdb=" CA PRO A 250 " pdb=" CB PRO A 250 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.59e+01 angle pdb=" C3' DG P 26 " pdb=" O3' DG P 26 " pdb=" P B DA P 27 " ideal model delta sigma weight residual 120.20 111.04 9.16 1.50e+00 4.44e-01 3.73e+01 angle pdb=" N ILE A 954 " pdb=" CA ILE A 954 " pdb=" C ILE A 954 " ideal model delta sigma weight residual 110.21 104.84 5.37 1.13e+00 7.83e-01 2.26e+01 ... (remaining 19827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.68: 8015 30.68 - 61.36: 487 61.36 - 92.04: 27 92.04 - 122.72: 0 122.72 - 153.41: 2 Dihedral angle restraints: 8531 sinusoidal: 3718 harmonic: 4813 Sorted by residual: dihedral pdb=" CA PRO A1070 " pdb=" C PRO A1070 " pdb=" N ARG A1071 " pdb=" CA ARG A1071 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CD ARG B 75 " pdb=" NE ARG B 75 " pdb=" CZ ARG B 75 " pdb=" NH1 ARG B 75 " ideal model delta sinusoidal sigma weight residual 0.00 -37.38 37.38 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA LEU B 393 " pdb=" C LEU B 393 " pdb=" N GLU B 394 " pdb=" CA GLU B 394 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2088 0.111 - 0.222: 49 0.222 - 0.333: 0 0.333 - 0.444: 0 0.444 - 0.555: 1 Chirality restraints: 2138 Sorted by residual: chirality pdb=" P DG P 26 " pdb=" OP1 DG P 26 " pdb=" OP2 DG P 26 " pdb=" O5' DG P 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA PRO A 625 " pdb=" N PRO A 625 " pdb=" C PRO A 625 " pdb=" CB PRO A 625 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA LEU A 605 " pdb=" N LEU A 605 " pdb=" C LEU A 605 " pdb=" CB LEU A 605 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2135 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 75 " 0.665 9.50e-02 1.11e+02 2.98e-01 5.43e+01 pdb=" NE ARG B 75 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 75 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 75 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 75 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 363 " 0.546 9.50e-02 1.11e+02 2.45e-01 3.66e+01 pdb=" NE ARG B 363 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 363 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 363 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 363 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 852 " -0.406 9.50e-02 1.11e+02 1.82e-01 2.03e+01 pdb=" NE ARG A 852 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 852 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 852 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 852 " -0.013 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 261 2.65 - 3.21: 13315 3.21 - 3.77: 22571 3.77 - 4.34: 30448 4.34 - 4.90: 49068 Nonbonded interactions: 115663 Sorted by model distance: nonbonded pdb=" OG SER C 90 " pdb=" O CYS C 95 " model vdw 2.085 3.040 nonbonded pdb=" O PRO A 857 " pdb=" OG1 THR A 861 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.121 3.040 nonbonded pdb=" O LYS A 553 " pdb=" NZ LYS A 553 " model vdw 2.122 3.120 nonbonded pdb=" N GLU A 280 " pdb=" OE1 GLU A 280 " model vdw 2.153 3.120 ... (remaining 115658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 68 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or resid 106 through 136 or re \ sid 180 through 219 or resid 227 through 355 or resid 368 through 420 or (resid \ 421 and (name N or name CA or name C or name O or name CB )) or resid 422 throug \ h 485)) selection = (chain 'C' and (resid 68 through 136 or resid 180 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 38.320 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 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 : 0.004 0.083 14516 Z= 0.256 Angle : 0.800 13.928 19832 Z= 0.433 Chirality : 0.044 0.555 2138 Planarity : 0.010 0.298 2416 Dihedral : 17.633 153.406 5427 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 1.33 % Allowed : 26.97 % Favored : 71.70 % 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: -0.24 (0.21), residues: 1643 helix: 1.15 (0.22), residues: 595 sheet: 0.04 (0.37), residues: 194 loop : -1.18 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1118 HIS 0.010 0.001 HIS C 313 PHE 0.037 0.001 PHE A 539 TYR 0.014 0.001 TYR A1108 ARG 0.013 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 539 PHE cc_start: 0.6585 (p90) cc_final: 0.5406 (p90) REVERT: A 579 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7730 (mmm160) REVERT: A 1195 MET cc_start: 0.7873 (ttm) cc_final: 0.7600 (ptp) REVERT: C 422 GLN cc_start: 0.5878 (tp-100) cc_final: 0.5364 (tp40) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 1.2716 time to fit residues: 329.1208 Evaluate side-chains 201 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 134 ASN A 138 HIS A 144 GLN A 226 GLN A 394 GLN A 472 GLN A 493 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 843 GLN ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 GLN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1102 GLN ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN B 305 ASN B 355 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14516 Z= 0.328 Angle : 0.733 12.535 19832 Z= 0.369 Chirality : 0.046 0.189 2138 Planarity : 0.005 0.051 2416 Dihedral : 15.095 150.917 2221 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 4.78 % Allowed : 23.31 % Favored : 71.91 % 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: -0.23 (0.21), residues: 1643 helix: 1.14 (0.21), residues: 607 sheet: -0.02 (0.35), residues: 208 loop : -1.19 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 607 HIS 0.009 0.001 HIS A1134 PHE 0.014 0.002 PHE B 266 TYR 0.014 0.002 TYR A1108 ARG 0.008 0.001 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 209 time to evaluate : 1.481 Fit side-chains REVERT: A 108 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 445 GLU cc_start: 0.8087 (pm20) cc_final: 0.7320 (pm20) REVERT: C 396 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7750 (mpp80) outliers start: 68 outliers final: 26 residues processed: 251 average time/residue: 1.2352 time to fit residues: 343.0537 Evaluate side-chains 208 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 HIS B 258 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14516 Z= 0.305 Angle : 0.711 11.718 19832 Z= 0.356 Chirality : 0.045 0.162 2138 Planarity : 0.005 0.048 2416 Dihedral : 15.165 150.663 2214 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 5.62 % Allowed : 23.81 % Favored : 70.58 % 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: -0.40 (0.21), residues: 1643 helix: 0.96 (0.21), residues: 618 sheet: -0.02 (0.35), residues: 194 loop : -1.30 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 607 HIS 0.009 0.001 HIS A1134 PHE 0.018 0.001 PHE A 610 TYR 0.011 0.001 TYR A1108 ARG 0.008 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7457 (tm-30) REVERT: A 1112 MET cc_start: 0.7988 (mtt) cc_final: 0.7682 (mtt) REVERT: B 386 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7456 (t70) REVERT: C 396 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7782 (mpp80) outliers start: 80 outliers final: 33 residues processed: 235 average time/residue: 1.2016 time to fit residues: 311.9617 Evaluate side-chains 212 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 HIS A1134 HIS A1222 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14516 Z= 0.255 Angle : 0.698 13.550 19832 Z= 0.346 Chirality : 0.044 0.159 2138 Planarity : 0.005 0.050 2416 Dihedral : 15.113 150.835 2210 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.76 % Rotamer: Outliers : 5.62 % Allowed : 24.44 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1643 helix: 1.07 (0.21), residues: 612 sheet: -0.02 (0.35), residues: 194 loop : -1.25 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 607 HIS 0.005 0.001 HIS A1134 PHE 0.010 0.001 PHE B 266 TYR 0.013 0.001 TYR A1108 ARG 0.006 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 188 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 550 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: A 1143 GLU cc_start: 0.7566 (pm20) cc_final: 0.7366 (pt0) REVERT: A 1208 ARG cc_start: 0.5449 (OUTLIER) cc_final: 0.5102 (ptt180) REVERT: C 396 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7765 (mpp80) outliers start: 80 outliers final: 33 residues processed: 238 average time/residue: 1.0183 time to fit residues: 267.6970 Evaluate side-chains 217 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14516 Z= 0.341 Angle : 0.744 11.670 19832 Z= 0.372 Chirality : 0.046 0.170 2138 Planarity : 0.005 0.053 2416 Dihedral : 15.228 151.601 2210 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.72 % Rotamer: Outliers : 6.46 % Allowed : 23.81 % Favored : 69.73 % 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: 1643 helix: 0.82 (0.21), residues: 624 sheet: -0.07 (0.35), residues: 194 loop : -1.39 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.013 0.002 PHE B 266 TYR 0.016 0.002 TYR B 193 ARG 0.006 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 182 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 594 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 1112 MET cc_start: 0.7954 (mtt) cc_final: 0.7577 (mtt) REVERT: A 1143 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: A 1208 ARG cc_start: 0.5478 (OUTLIER) cc_final: 0.5034 (ptt180) REVERT: C 396 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7796 (mpp80) outliers start: 92 outliers final: 42 residues processed: 242 average time/residue: 1.1347 time to fit residues: 304.5313 Evaluate side-chains 214 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1202 ASN Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0050 chunk 146 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14516 Z= 0.203 Angle : 0.705 14.668 19832 Z= 0.348 Chirality : 0.043 0.211 2138 Planarity : 0.005 0.065 2416 Dihedral : 15.141 150.785 2210 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 4.92 % Allowed : 25.21 % Favored : 69.87 % 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: -0.39 (0.21), residues: 1643 helix: 0.94 (0.21), residues: 623 sheet: -0.01 (0.36), residues: 197 loop : -1.29 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 607 HIS 0.005 0.001 HIS B 77 PHE 0.009 0.001 PHE B 254 TYR 0.019 0.001 TYR B 432 ARG 0.011 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 228 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.4911 (tp) REVERT: A 550 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6113 (mp10) REVERT: A 774 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7748 (ptm) REVERT: A 1143 GLU cc_start: 0.7272 (pm20) cc_final: 0.6592 (pt0) REVERT: C 396 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7781 (mpp80) outliers start: 70 outliers final: 36 residues processed: 239 average time/residue: 1.2366 time to fit residues: 325.8818 Evaluate side-chains 215 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 550 GLN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** A 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14516 Z= 0.314 Angle : 0.750 14.605 19832 Z= 0.372 Chirality : 0.045 0.232 2138 Planarity : 0.005 0.048 2416 Dihedral : 15.219 151.569 2210 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 5.27 % Allowed : 25.70 % Favored : 69.03 % 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: -0.45 (0.21), residues: 1643 helix: 0.89 (0.21), residues: 620 sheet: -0.02 (0.36), residues: 200 loop : -1.33 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 607 HIS 0.005 0.001 HIS C 454 PHE 0.015 0.001 PHE A 610 TYR 0.018 0.002 TYR A 573 ARG 0.004 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 175 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 228 LEU cc_start: 0.5550 (OUTLIER) cc_final: 0.5035 (tp) REVERT: A 1112 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: C 396 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7815 (mpp80) outliers start: 75 outliers final: 45 residues processed: 224 average time/residue: 1.1857 time to fit residues: 295.2529 Evaluate side-chains 210 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14516 Z= 0.215 Angle : 0.731 13.680 19832 Z= 0.358 Chirality : 0.043 0.206 2138 Planarity : 0.004 0.046 2416 Dihedral : 15.185 150.745 2210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 3.44 % Allowed : 27.53 % Favored : 69.03 % 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: -0.40 (0.21), residues: 1643 helix: 0.88 (0.21), residues: 624 sheet: 0.06 (0.36), residues: 197 loop : -1.27 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 607 HIS 0.006 0.001 HIS B 77 PHE 0.010 0.001 PHE C 403 TYR 0.021 0.001 TYR B 193 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 228 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.4912 (tp) REVERT: C 396 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7773 (mpp80) outliers start: 49 outliers final: 37 residues processed: 213 average time/residue: 1.1420 time to fit residues: 270.0599 Evaluate side-chains 204 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.0670 chunk 65 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.0060 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 740 ASN ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14516 Z= 0.189 Angle : 0.722 13.369 19832 Z= 0.354 Chirality : 0.043 0.201 2138 Planarity : 0.004 0.044 2416 Dihedral : 15.111 150.498 2210 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.12 % Favored : 92.82 % Rotamer: Outliers : 3.51 % Allowed : 28.37 % Favored : 68.12 % 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: -0.20 (0.21), residues: 1643 helix: 1.08 (0.21), residues: 620 sheet: 0.11 (0.36), residues: 197 loop : -1.15 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 607 HIS 0.006 0.001 HIS A 828 PHE 0.010 0.001 PHE C 403 TYR 0.019 0.001 TYR B 193 ARG 0.006 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 1.620 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 396 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7765 (mpp80) outliers start: 50 outliers final: 32 residues processed: 216 average time/residue: 1.1604 time to fit residues: 278.0441 Evaluate side-chains 203 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 323 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14516 Z= 0.357 Angle : 0.789 13.341 19832 Z= 0.392 Chirality : 0.047 0.210 2138 Planarity : 0.005 0.049 2416 Dihedral : 15.252 151.906 2210 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 3.37 % Allowed : 28.65 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.21), residues: 1643 helix: 0.78 (0.21), residues: 626 sheet: -0.01 (0.35), residues: 202 loop : -1.33 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 607 HIS 0.006 0.001 HIS A 84 PHE 0.042 0.002 PHE A 539 TYR 0.021 0.002 TYR A 573 ARG 0.005 0.001 ARG A 853 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.606 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 540 GLN cc_start: 0.7668 (mp10) cc_final: 0.7430 (pm20) REVERT: C 396 ARG cc_start: 0.8267 (tpp-160) cc_final: 0.7768 (mpp80) outliers start: 48 outliers final: 40 residues processed: 204 average time/residue: 1.1630 time to fit residues: 263.3218 Evaluate side-chains 203 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1057 MET Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1163 MET Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1206 MET Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 459 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 975 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.151679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.119815 restraints weight = 27004.620| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.40 r_work: 0.3589 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14516 Z= 0.239 Angle : 0.751 13.662 19832 Z= 0.373 Chirality : 0.044 0.195 2138 Planarity : 0.004 0.045 2416 Dihedral : 15.244 151.443 2210 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 3.02 % Allowed : 29.07 % Favored : 67.91 % 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: -0.46 (0.21), residues: 1643 helix: 0.77 (0.21), residues: 628 sheet: 0.06 (0.36), residues: 197 loop : -1.27 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 607 HIS 0.007 0.001 HIS B 77 PHE 0.011 0.001 PHE C 403 TYR 0.017 0.001 TYR A 573 ARG 0.010 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5483.59 seconds wall clock time: 110 minutes 40.30 seconds (6640.30 seconds total)