Starting phenix.real_space_refine on Sun Nov 17 19:13:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5j_29746/11_2024/8g5j_29746_neut.cif" } resolution = 2.63 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= 0.026 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 40 5.49 5 S 80 5.16 5 C 9131 2.51 5 N 2562 2.21 5 O 2731 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-5513/modules/chem_data/mon_lib" Total number of atoms: 14544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7369 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 60, 'TRANS': 880} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 4, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3188 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 379} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "P" Number of atoms: 413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} 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: 19, 393 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} 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: 419 Chain: "T" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA P 28 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 28 " occ=0.50 residue: pdb=" P DG T 3 " occ=0.50 ... (20 atoms not shown) pdb=" C4 DG T 3 " occ=0.50 Time building chain proxies: 8.76, per 1000 atoms: 0.60 Number of scatterers: 14544 At special positions: 0 Unit cell: (102.424, 102.424, 145.376, 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 40 15.00 O 2731 8.00 N 2562 7.00 C 9131 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: 3.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3242 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 41.1% alpha, 12.2% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.509A pdb=" N GLU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix 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: 6.890A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.725A pdb=" N GLY A 303 " --> pdb=" O MET A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 316 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: 4.063A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.501A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 4.007A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 537 through 548 Processing helix chain 'A' and resid 551 through 556 removed outlier: 4.041A pdb=" N THR A 555 " --> pdb=" O LYS A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.002A pdb=" N LYS A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 777 Processing helix chain 'A' and resid 786 through 810 removed outlier: 4.719A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.597A pdb=" N ILE A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 853 removed outlier: 4.166A pdb=" N ARG A 853 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 901 Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.503A pdb=" N THR A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 954 removed outlier: 4.629A pdb=" N GLY A 952 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 971 Processing helix chain 'A' and resid 973 through 984 removed outlier: 4.264A pdb=" N LYS A 981 " --> pdb=" O GLU A 977 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA A 982 " --> pdb=" O ALA A 978 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1057 through 1066 removed outlier: 4.029A pdb=" N LEU A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.762A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 Processing helix chain 'A' and resid 1216 through 1221 removed outlier: 3.624A pdb=" N ASP A1219 " --> pdb=" O GLU A1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 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 192 Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.515A pdb=" N VAL B 200 " --> pdb=" O CYS B 196 " (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 Processing helix chain 'B' and resid 319 through 323 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 409 removed outlier: 4.062A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.918A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.794A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 199 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 200 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.158A 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 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.982A pdb=" N LEU C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.584A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 removed outlier: 4.590A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.808A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 211 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU A 200 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN A 264 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 292 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 6.326A 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 438 removed outlier: 4.689A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1130 through 1133 Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.294A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.087A 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 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 415 removed outlier: 7.157A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.516A 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: 6.263A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.865A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 4.41 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: 4473 1.34 - 1.46: 2636 1.46 - 1.58: 7664 1.58 - 1.70: 79 1.70 - 1.82: 126 Bond restraints: 14978 Sorted by residual: bond pdb=" P DC T 4 " pdb=" OP2 DC T 4 " ideal model delta sigma weight residual 1.480 1.621 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C2' DG T 3 " pdb=" C1' DG T 3 " ideal model delta sigma weight residual 1.525 1.438 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1' DA P 15 " pdb=" N9 DA P 15 " ideal model delta sigma weight residual 1.460 1.381 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1' DG P 16 " pdb=" N9 DG P 16 " ideal model delta sigma weight residual 1.460 1.382 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1' DG T 13 " pdb=" N9 DG T 13 " ideal model delta sigma weight residual 1.460 1.387 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 14973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 20371 5.44 - 10.87: 90 10.87 - 16.31: 8 16.31 - 21.74: 0 21.74 - 27.18: 1 Bond angle restraints: 20470 Sorted by residual: angle pdb=" C3' DG T 3 " pdb=" O3' DG T 3 " pdb=" P DC T 4 " ideal model delta sigma weight residual 120.20 93.02 27.18 1.50e+00 4.44e-01 3.28e+02 angle pdb=" C4' DG T 3 " pdb=" C3' DG T 3 " pdb=" O3' DG T 3 " ideal model delta sigma weight residual 110.00 125.79 -15.79 1.50e+00 4.44e-01 1.11e+02 angle pdb=" O3' DG T 3 " pdb=" C3' DG T 3 " pdb=" C2' DG T 3 " ideal model delta sigma weight residual 111.50 96.44 15.06 1.50e+00 4.44e-01 1.01e+02 angle pdb=" N PRO C 137 " pdb=" CA PRO C 137 " pdb=" C PRO C 137 " ideal model delta sigma weight residual 113.65 100.84 12.81 1.35e+00 5.49e-01 9.00e+01 angle pdb=" C3' DC T 2 " pdb=" O3' DC T 2 " pdb=" P DG T 3 " ideal model delta sigma weight residual 120.20 107.81 12.39 1.50e+00 4.44e-01 6.83e+01 ... (remaining 20465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 8082 28.66 - 57.32: 668 57.32 - 85.97: 81 85.97 - 114.63: 0 114.63 - 143.29: 3 Dihedral angle restraints: 8834 sinusoidal: 3819 harmonic: 5015 Sorted by residual: dihedral pdb=" CD ARG A 102 " pdb=" NE ARG A 102 " pdb=" CZ ARG A 102 " pdb=" NH1 ARG A 102 " ideal model delta sinusoidal sigma weight residual 0.00 -69.84 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" CD ARG B 257 " pdb=" NE ARG B 257 " pdb=" CZ ARG B 257 " pdb=" NH1 ARG B 257 " ideal model delta sinusoidal sigma weight residual 0.00 -57.20 57.20 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CD ARG B 154 " pdb=" NE ARG B 154 " pdb=" CZ ARG B 154 " pdb=" NH1 ARG B 154 " ideal model delta sinusoidal sigma weight residual 0.00 55.71 -55.71 1 1.00e+01 1.00e-02 4.19e+01 ... (remaining 8831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 2195 0.236 - 0.472: 24 0.472 - 0.708: 8 0.708 - 0.944: 0 0.944 - 1.179: 1 Chirality restraints: 2228 Sorted by residual: chirality pdb=" P DC T 4 " pdb=" OP1 DC T 4 " pdb=" OP2 DC T 4 " pdb=" O5' DC T 4 " both_signs ideal model delta sigma weight residual True 2.35 -3.53 -1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" P DC T 2 " pdb=" OP1 DC T 2 " pdb=" OP2 DC T 2 " pdb=" O5' DC T 2 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA P 10 " pdb=" OP1 DA P 10 " pdb=" OP2 DA P 10 " pdb=" O5' DA P 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.15e+00 ... (remaining 2225 not shown) Planarity restraints: 2497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 102 " -1.036 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG A 102 " 0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 102 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 102 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 102 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 257 " -0.923 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG B 257 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG B 257 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 257 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 257 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 154 " -0.904 9.50e-02 1.11e+02 4.05e-01 9.96e+01 pdb=" NE ARG B 154 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 154 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 154 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 154 " -0.024 2.00e-02 2.50e+03 ... (remaining 2494 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 283 2.67 - 3.22: 13525 3.22 - 3.78: 23408 3.78 - 4.34: 31799 4.34 - 4.90: 51352 Nonbonded interactions: 120367 Sorted by model distance: nonbonded pdb=" OD2 ASP A 892 " pdb=" OG SER A1181 " model vdw 2.108 3.040 nonbonded pdb=" NH2 ARG B 75 " pdb=" O GLY B 81 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR A 885 " pdb=" O ASP A1186 " model vdw 2.179 3.040 nonbonded pdb=" O ASP A 491 " pdb=" NH2 ARG A 574 " model vdw 2.220 3.120 nonbonded pdb=" C2' DG T 3 " pdb=" P DC T 4 " model vdw 2.229 3.040 ... (remaining 120362 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 (r \ esid 137 and (name N or name CA or name C or name O )) or resid 138 through 219 \ or resid 229 through 283 or (resid 284 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 355 or resid 368 through 485)) selection = (chain 'C' and (resid 68 through 161 or (resid 169 through 178 and (name N or na \ me CA or name C or name O or name CB )) or resid 179 through 219 or resid 229 th \ rough 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.890 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 0.141 14978 Z= 0.372 Angle : 1.039 27.179 20470 Z= 0.600 Chirality : 0.076 1.179 2228 Planarity : 0.021 0.464 2497 Dihedral : 19.274 143.288 5592 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 2.20 % Allowed : 25.14 % Favored : 72.66 % 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: -0.53 (0.20), residues: 1713 helix: 1.05 (0.21), residues: 658 sheet: 0.29 (0.33), residues: 228 loop : -1.78 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 607 HIS 0.016 0.001 HIS C 309 PHE 0.039 0.001 PHE A 961 TYR 0.018 0.001 TYR C 291 ARG 0.024 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 1.671 Fit side-chains REVERT: A 87 ILE cc_start: 0.2050 (OUTLIER) cc_final: 0.1459 (pp) REVERT: A 215 ILE cc_start: 0.7484 (pt) cc_final: 0.7283 (pt) REVERT: B 329 LYS cc_start: 0.7431 (ptmm) cc_final: 0.7196 (ptmt) REVERT: B 460 THR cc_start: 0.7615 (p) cc_final: 0.7225 (p) REVERT: C 397 GLN cc_start: 0.7095 (mp10) cc_final: 0.6506 (mp10) outliers start: 32 outliers final: 12 residues processed: 207 average time/residue: 1.2157 time to fit residues: 279.8909 Evaluate side-chains 172 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 144 GLN A 550 GLN A 761 ASN A 811 GLN A 843 GLN A 894 GLN A 922 GLN A1059 ASN A1089 GLN A1110 HIS A1222 GLN B 133 HIS B 187 HIS B 272 ASN C 250 GLN C 279 GLN C 309 HIS C 330 ASN C 404 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14978 Z= 0.323 Angle : 0.701 11.870 20470 Z= 0.362 Chirality : 0.047 0.264 2228 Planarity : 0.006 0.067 2497 Dihedral : 16.462 145.517 2313 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.95 % Favored : 93.87 % Rotamer: Outliers : 3.91 % Allowed : 24.11 % Favored : 71.98 % 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: -0.41 (0.20), residues: 1713 helix: 1.16 (0.21), residues: 656 sheet: 0.45 (0.32), residues: 238 loop : -1.77 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 748 HIS 0.008 0.001 HIS A 84 PHE 0.019 0.002 PHE A 610 TYR 0.015 0.002 TYR C 291 ARG 0.013 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 1.545 Fit side-chains REVERT: A 87 ILE cc_start: 0.2034 (OUTLIER) cc_final: 0.1420 (pp) REVERT: A 183 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: A 372 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: A 484 TRP cc_start: 0.7973 (m-90) cc_final: 0.7116 (m-10) REVERT: C 355 GLN cc_start: 0.5297 (OUTLIER) cc_final: 0.4065 (pm20) outliers start: 57 outliers final: 23 residues processed: 204 average time/residue: 1.2003 time to fit residues: 272.1839 Evaluate side-chains 175 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 158 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 550 GLN A 803 ASN A1102 GLN C 309 HIS C 409 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14978 Z= 0.204 Angle : 0.616 9.622 20470 Z= 0.318 Chirality : 0.043 0.152 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.370 146.721 2307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.30 % Favored : 93.52 % Rotamer: Outliers : 3.71 % Allowed : 24.66 % Favored : 71.63 % 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: -0.26 (0.20), residues: 1713 helix: 1.31 (0.21), residues: 656 sheet: 0.50 (0.33), residues: 238 loop : -1.69 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 PHE 0.014 0.001 PHE A 766 TYR 0.011 0.001 TYR A1108 ARG 0.013 0.001 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.2057 (OUTLIER) cc_final: 0.1449 (pp) REVERT: A 108 GLN cc_start: 0.7314 (tt0) cc_final: 0.7083 (mt0) REVERT: A 120 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (tp) REVERT: A 183 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: A 372 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: A 603 MET cc_start: 0.4476 (OUTLIER) cc_final: 0.4024 (ppp) REVERT: A 910 MET cc_start: 0.8113 (mpp) cc_final: 0.7816 (mpt) REVERT: A 1131 ILE cc_start: 0.4060 (OUTLIER) cc_final: 0.3629 (mt) REVERT: B 314 MET cc_start: 0.8740 (ttm) cc_final: 0.8479 (mtp) REVERT: C 355 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.3989 (pm20) REVERT: C 400 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7536 (tm-30) outliers start: 54 outliers final: 24 residues processed: 196 average time/residue: 1.1762 time to fit residues: 256.3718 Evaluate side-chains 187 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 152 optimal weight: 0.0870 chunk 45 optimal weight: 0.0870 chunk 141 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 564 GLN A 803 ASN A 828 HIS B 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14978 Z= 0.170 Angle : 0.586 13.826 20470 Z= 0.302 Chirality : 0.042 0.325 2228 Planarity : 0.005 0.061 2497 Dihedral : 16.245 146.706 2306 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.25 % Favored : 93.58 % Rotamer: Outliers : 3.91 % Allowed : 24.73 % Favored : 71.36 % 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: -0.16 (0.20), residues: 1713 helix: 1.35 (0.21), residues: 669 sheet: 0.68 (0.33), residues: 232 loop : -1.68 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 241 HIS 0.006 0.001 HIS C 77 PHE 0.013 0.001 PHE A 766 TYR 0.018 0.001 TYR C 206 ARG 0.008 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.1817 (OUTLIER) cc_final: 0.1207 (pp) REVERT: A 108 GLN cc_start: 0.7318 (tt0) cc_final: 0.6802 (mt0) REVERT: A 120 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8657 (tp) REVERT: A 183 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: A 372 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6463 (mt-10) REVERT: A 484 TRP cc_start: 0.7899 (m-90) cc_final: 0.7107 (m-10) REVERT: A 603 MET cc_start: 0.4508 (OUTLIER) cc_final: 0.3992 (ppp) REVERT: A 780 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6845 (mt0) REVERT: A 910 MET cc_start: 0.8036 (mpp) cc_final: 0.7743 (mpt) REVERT: A 1131 ILE cc_start: 0.4146 (OUTLIER) cc_final: 0.3709 (mt) REVERT: B 460 THR cc_start: 0.7852 (p) cc_final: 0.7562 (p) REVERT: C 400 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7515 (tm-30) outliers start: 57 outliers final: 22 residues processed: 205 average time/residue: 1.1616 time to fit residues: 266.6061 Evaluate side-chains 186 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 183 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 126 optimal weight: 0.0870 chunk 70 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 550 GLN A 803 ASN B 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14978 Z= 0.181 Angle : 0.588 11.799 20470 Z= 0.303 Chirality : 0.042 0.199 2228 Planarity : 0.005 0.060 2497 Dihedral : 16.219 146.390 2305 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.10 % Rotamer: Outliers : 3.98 % Allowed : 24.86 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1713 helix: 1.36 (0.21), residues: 669 sheet: 0.71 (0.34), residues: 232 loop : -1.64 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 PHE 0.025 0.001 PHE A 961 TYR 0.018 0.001 TYR C 193 ARG 0.008 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 159 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.1767 (OUTLIER) cc_final: 0.1121 (pp) REVERT: A 108 GLN cc_start: 0.7377 (tt0) cc_final: 0.6892 (mt0) REVERT: A 120 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 372 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: A 442 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: A 484 TRP cc_start: 0.7848 (m-90) cc_final: 0.7052 (m-10) REVERT: A 603 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.4138 (ppp) REVERT: A 780 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6905 (mt0) REVERT: A 910 MET cc_start: 0.7994 (mpp) cc_final: 0.7658 (mpt) REVERT: A 947 LYS cc_start: 0.7312 (tptt) cc_final: 0.6679 (ttmt) REVERT: A 1131 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3718 (mt) REVERT: B 314 MET cc_start: 0.8766 (ttm) cc_final: 0.8508 (mtp) REVERT: B 460 THR cc_start: 0.7822 (p) cc_final: 0.7564 (p) REVERT: C 400 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7531 (tm-30) outliers start: 58 outliers final: 25 residues processed: 197 average time/residue: 1.2023 time to fit residues: 263.6824 Evaluate side-chains 187 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 780 GLN Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.0470 chunk 164 optimal weight: 2.9990 overall best weight: 0.7290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14978 Z= 0.190 Angle : 0.590 11.132 20470 Z= 0.304 Chirality : 0.042 0.170 2228 Planarity : 0.005 0.064 2497 Dihedral : 16.210 146.384 2305 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.42 % Favored : 93.40 % Rotamer: Outliers : 4.12 % Allowed : 24.86 % Favored : 71.02 % 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: -0.12 (0.21), residues: 1713 helix: 1.36 (0.21), residues: 669 sheet: 0.73 (0.34), residues: 233 loop : -1.65 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 748 HIS 0.006 0.001 HIS B 77 PHE 0.029 0.001 PHE A 961 TYR 0.012 0.001 TYR C 193 ARG 0.008 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 87 ILE cc_start: 0.1777 (OUTLIER) cc_final: 0.1118 (pp) REVERT: A 108 GLN cc_start: 0.7391 (tt0) cc_final: 0.6913 (mt0) REVERT: A 372 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: A 442 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: A 484 TRP cc_start: 0.7836 (m-90) cc_final: 0.7077 (m-10) REVERT: A 603 MET cc_start: 0.4485 (OUTLIER) cc_final: 0.4212 (ppp) REVERT: A 910 MET cc_start: 0.8016 (mpp) cc_final: 0.7700 (mpt) REVERT: A 947 LYS cc_start: 0.7251 (tptt) cc_final: 0.6729 (ttmt) REVERT: A 1131 ILE cc_start: 0.4129 (OUTLIER) cc_final: 0.3663 (mt) REVERT: B 256 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7817 (tp) REVERT: B 314 MET cc_start: 0.8780 (ttm) cc_final: 0.8519 (mtp) REVERT: B 460 THR cc_start: 0.7817 (p) cc_final: 0.7572 (p) REVERT: C 355 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4021 (pm20) REVERT: C 400 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: C 465 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7871 (mmm) outliers start: 60 outliers final: 24 residues processed: 202 average time/residue: 1.2013 time to fit residues: 269.6921 Evaluate side-chains 184 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 355 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 465 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0070 chunk 97 optimal weight: 0.6980 chunk 124 optimal weight: 0.0070 chunk 96 optimal weight: 0.9990 chunk 143 optimal weight: 0.3980 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 803 ASN C 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14978 Z= 0.164 Angle : 0.574 10.596 20470 Z= 0.296 Chirality : 0.041 0.145 2228 Planarity : 0.004 0.063 2497 Dihedral : 16.145 146.307 2305 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 3.64 % Allowed : 26.37 % Favored : 69.99 % 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: -0.02 (0.21), residues: 1713 helix: 1.47 (0.21), residues: 670 sheet: 0.76 (0.34), residues: 233 loop : -1.61 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 918 HIS 0.006 0.001 HIS C 309 PHE 0.028 0.001 PHE A 961 TYR 0.012 0.001 TYR C 193 ARG 0.006 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ILE cc_start: 0.1685 (OUTLIER) cc_final: 0.1062 (pp) REVERT: A 108 GLN cc_start: 0.7392 (tt0) cc_final: 0.6803 (mt0) REVERT: A 372 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: A 442 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: A 890 ASP cc_start: 0.7849 (p0) cc_final: 0.7620 (p0) REVERT: A 947 LYS cc_start: 0.7234 (tptt) cc_final: 0.6752 (ttmt) REVERT: A 1131 ILE cc_start: 0.4123 (OUTLIER) cc_final: 0.3672 (mt) REVERT: B 124 GLN cc_start: 0.5703 (mm-40) cc_final: 0.5464 (mm-40) REVERT: B 314 MET cc_start: 0.8753 (ttm) cc_final: 0.8504 (mtp) REVERT: C 397 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: C 400 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7534 (tm-30) outliers start: 53 outliers final: 19 residues processed: 200 average time/residue: 1.2335 time to fit residues: 275.4326 Evaluate side-chains 180 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.0070 chunk 101 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 0.0770 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 550 GLN A 803 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14978 Z= 0.168 Angle : 0.583 10.242 20470 Z= 0.298 Chirality : 0.041 0.185 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.146 146.183 2303 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.13 % Favored : 93.70 % Rotamer: Outliers : 2.47 % Allowed : 27.47 % Favored : 70.05 % 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: -0.02 (0.21), residues: 1713 helix: 1.46 (0.21), residues: 670 sheet: 0.80 (0.34), residues: 233 loop : -1.62 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 918 HIS 0.005 0.001 HIS B 77 PHE 0.028 0.001 PHE A 961 TYR 0.013 0.001 TYR C 193 ARG 0.008 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7373 (tt0) cc_final: 0.6819 (mt0) REVERT: A 120 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 372 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6514 (mt-10) REVERT: A 442 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: A 603 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.4168 (ppp) REVERT: A 890 ASP cc_start: 0.7862 (p0) cc_final: 0.7621 (p0) REVERT: A 910 MET cc_start: 0.8034 (mpp) cc_final: 0.7734 (mpt) REVERT: A 947 LYS cc_start: 0.7201 (tptt) cc_final: 0.6741 (ttmt) REVERT: A 1131 ILE cc_start: 0.4112 (OUTLIER) cc_final: 0.3650 (mt) REVERT: B 124 GLN cc_start: 0.5734 (mm-40) cc_final: 0.5494 (mm-40) REVERT: B 314 MET cc_start: 0.8760 (ttm) cc_final: 0.8504 (mtp) REVERT: C 397 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6857 (mp10) REVERT: C 400 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7547 (tm-30) outliers start: 36 outliers final: 17 residues processed: 180 average time/residue: 1.1975 time to fit residues: 239.5953 Evaluate side-chains 178 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1227 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 158 optimal weight: 0.3980 chunk 95 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.0570 chunk 48 optimal weight: 0.3980 chunk 142 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 550 GLN A 803 ASN A 805 HIS C 309 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14978 Z= 0.156 Angle : 0.577 10.820 20470 Z= 0.295 Chirality : 0.041 0.159 2228 Planarity : 0.005 0.063 2497 Dihedral : 16.113 146.040 2301 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 2.54 % Allowed : 27.61 % Favored : 69.85 % 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: 0.04 (0.21), residues: 1713 helix: 1.53 (0.21), residues: 670 sheet: 0.82 (0.34), residues: 232 loop : -1.60 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 918 HIS 0.006 0.001 HIS C 309 PHE 0.028 0.001 PHE A 961 TYR 0.013 0.001 TYR C 193 ARG 0.018 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.632 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7400 (tt0) cc_final: 0.6886 (mt0) REVERT: A 120 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8615 (tp) REVERT: A 191 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: A 372 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6471 (mt-10) REVERT: A 442 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: A 603 MET cc_start: 0.4550 (OUTLIER) cc_final: 0.4144 (ppp) REVERT: A 890 ASP cc_start: 0.7894 (p0) cc_final: 0.7651 (p0) REVERT: A 910 MET cc_start: 0.7980 (mpp) cc_final: 0.7700 (mpt) REVERT: A 947 LYS cc_start: 0.7193 (tptt) cc_final: 0.6730 (ttmt) REVERT: A 1131 ILE cc_start: 0.4055 (OUTLIER) cc_final: 0.3596 (mt) REVERT: A 1218 LEU cc_start: 0.7853 (pp) cc_final: 0.7590 (pp) REVERT: B 124 GLN cc_start: 0.5655 (mm-40) cc_final: 0.5417 (mm-40) REVERT: B 314 MET cc_start: 0.8756 (ttm) cc_final: 0.8500 (mtp) REVERT: B 460 THR cc_start: 0.7746 (p) cc_final: 0.7473 (p) REVERT: C 397 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 400 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7794 (tp-100) outliers start: 37 outliers final: 17 residues processed: 183 average time/residue: 1.1677 time to fit residues: 238.3166 Evaluate side-chains 176 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 397 GLN Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 161 optimal weight: 0.0570 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 298 HIS A 550 GLN A 803 ASN A 984 GLN C 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14978 Z= 0.182 Angle : 0.593 10.187 20470 Z= 0.302 Chirality : 0.041 0.162 2228 Planarity : 0.005 0.065 2497 Dihedral : 16.146 146.092 2301 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.25 % Favored : 93.58 % Rotamer: Outliers : 2.06 % Allowed : 28.09 % Favored : 69.85 % 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: 0.02 (0.21), residues: 1713 helix: 1.51 (0.21), residues: 670 sheet: 0.86 (0.34), residues: 232 loop : -1.61 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 918 HIS 0.008 0.001 HIS A 269 PHE 0.029 0.001 PHE A 961 TYR 0.011 0.001 TYR C 193 ARG 0.013 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7383 (tt0) cc_final: 0.6893 (mt0) REVERT: A 126 ARG cc_start: 0.7446 (mmp-170) cc_final: 0.7197 (tpp-160) REVERT: A 191 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: A 372 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: A 442 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: A 812 MET cc_start: 0.7500 (ttt) cc_final: 0.7202 (ttt) REVERT: A 890 ASP cc_start: 0.7875 (p0) cc_final: 0.7618 (p0) REVERT: A 910 MET cc_start: 0.7991 (mpp) cc_final: 0.7786 (mpt) REVERT: A 947 LYS cc_start: 0.7201 (tptt) cc_final: 0.6733 (ttmt) REVERT: A 1131 ILE cc_start: 0.4135 (OUTLIER) cc_final: 0.3669 (mt) REVERT: B 124 GLN cc_start: 0.5685 (mm-40) cc_final: 0.5444 (mm-40) REVERT: B 314 MET cc_start: 0.8778 (ttm) cc_final: 0.8523 (mtp) REVERT: B 460 THR cc_start: 0.7782 (p) cc_final: 0.7502 (p) REVERT: C 400 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7540 (tm-30) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 1.2492 time to fit residues: 238.6851 Evaluate side-chains 174 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 HIS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 400 GLN Chi-restraints excluded: chain C residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 143 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 550 GLN A 803 ASN A 911 HIS A1214 GLN C 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.185707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133193 restraints weight = 37430.351| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.95 r_work: 0.3488 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14978 Z= 0.241 Angle : 0.631 10.695 20470 Z= 0.321 Chirality : 0.043 0.191 2228 Planarity : 0.005 0.063 2497 Dihedral : 16.257 146.427 2301 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.89 % Favored : 92.94 % Rotamer: Outliers : 2.13 % Allowed : 28.09 % Favored : 69.78 % 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: -0.12 (0.21), residues: 1713 helix: 1.37 (0.21), residues: 669 sheet: 0.80 (0.34), residues: 233 loop : -1.67 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 918 HIS 0.006 0.001 HIS A 613 PHE 0.030 0.002 PHE A 961 TYR 0.015 0.002 TYR A 233 ARG 0.013 0.001 ARG A 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5280.44 seconds wall clock time: 95 minutes 27.09 seconds (5727.09 seconds total)