Starting phenix.real_space_refine on Thu Aug 6 06:39:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8u_36962/08_2026/8k8u_36962.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.109 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 3 5.21 5 S 71 5.16 5 C 8860 2.51 5 N 2327 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13969 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8201 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 37, 'TRANS': 966} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "C" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3411 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain breaks: 1 Chain: "E" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 231 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 321 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 33 Unusual residues: {' MG': 3, 'CTP': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.08, per 1000 atoms: 0.22 Number of scatterers: 13969 At special positions: 0 Unit cell: (102.178, 127.179, 144.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 29 15.00 Mg 3 11.99 O 2679 8.00 N 2327 7.00 C 8860 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: 1.02 Conformation dependent library (CDL) restraints added in 629.4 milliseconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 19 sheets defined 40.1% alpha, 22.1% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.791A pdb=" N LEU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.515A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.756A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.882A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 552 through 562 removed outlier: 3.636A pdb=" N ASN A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 576 through 591 removed outlier: 4.215A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 643 removed outlier: 4.074A pdb=" N ARG A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 4.481A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 764 through 782 Processing helix chain 'A' and resid 837 through 857 Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.110A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.812A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 38 removed outlier: 4.038A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER B 35 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.502A pdb=" N GLN B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.955A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.895A pdb=" N HIS B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 188' Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.545A pdb=" N ASN B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.782A pdb=" N SER C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.737A pdb=" N ARG C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 177 through 187 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.749A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.714A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 341 through 351 removed outlier: 3.504A pdb=" N LYS C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.718A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 373 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.811A pdb=" N CYS C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.607A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.770A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.806A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.478A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.741A pdb=" N ILE A 614 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 571 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 612 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 573 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 610 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.544A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A 168 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 186 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA A 166 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 188 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE A 164 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR A 190 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 162 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 removed outlier: 6.507A pdb=" N TYR A 300 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE A 318 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 302 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR A 316 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 304 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 363 removed outlier: 6.622A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS A 404 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.506A pdb=" N PHE A 743 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 removed outlier: 4.657A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.649A pdb=" N VAL B 64 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB5, first strand: chain 'C' and resid 69 through 71 removed outlier: 3.519A pdb=" N THR C 174 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 166 through 169 removed outlier: 4.134A pdb=" N LEU C 166 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 78 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.774A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 214 through 227 removed outlier: 4.542A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 304 Processing sheet with id=AC1, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.638A pdb=" N ARG C 376 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 387 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 378 " --> pdb=" O VAL C 385 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2500 1.32 - 1.44: 3767 1.44 - 1.57: 7893 1.57 - 1.69: 56 1.69 - 1.81: 108 Bond restraints: 14324 Sorted by residual: bond pdb=" O3B CTP A1104 " pdb=" PG CTP A1104 " ideal model delta sigma weight residual 1.751 1.604 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" N PRO C 73 " pdb=" CD PRO C 73 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N PRO B 44 " pdb=" CD PRO B 44 " ideal model delta sigma weight residual 1.474 1.424 0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C ASP C 72 " pdb=" N PRO C 73 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" O3A CTP A1104 " pdb=" PB CTP A1104 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 14319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19056 1.93 - 3.86: 369 3.86 - 5.79: 40 5.79 - 7.71: 9 7.71 - 9.64: 3 Bond angle restraints: 19477 Sorted by residual: angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT F 5 " pdb=" C4 DT F 5 " pdb=" O4 DT F 5 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" O4 DT E 18 " pdb=" C4 DT E 18 " pdb=" C5 DT E 18 " ideal model delta sigma weight residual 124.90 122.02 2.88 7.00e-01 2.04e+00 1.69e+01 angle pdb=" N3 DT F 15 " pdb=" C4 DT F 15 " pdb=" O4 DT F 15 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT E 23 " pdb=" C4 DT E 23 " pdb=" O4 DT E 23 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 ... (remaining 19472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8157 17.83 - 35.66: 275 35.66 - 53.49: 126 53.49 - 71.32: 37 71.32 - 89.15: 6 Dihedral angle restraints: 8601 sinusoidal: 3730 harmonic: 4871 Sorted by residual: dihedral pdb=" CA TYR A 188 " pdb=" C TYR A 188 " pdb=" N CYS A 189 " pdb=" CA CYS A 189 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL A 310 " pdb=" C VAL A 310 " pdb=" N CYS A 311 " pdb=" CA CYS A 311 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA SER A 126 " pdb=" C SER A 126 " pdb=" N LEU A 127 " pdb=" CA LEU A 127 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1363 0.035 - 0.070: 338 0.070 - 0.106: 255 0.106 - 0.141: 142 0.141 - 0.176: 55 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA VAL B 77 " pdb=" N VAL B 77 " pdb=" C VAL B 77 " pdb=" CB VAL B 77 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" C1' CTP A1104 " pdb=" C2' CTP A1104 " pdb=" N1 CTP A1104 " pdb=" O4' CTP A1104 " both_signs ideal model delta sigma weight residual False 2.35 2.53 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2150 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CTP A1104 " 0.248 2.00e-02 2.50e+03 1.41e-01 4.45e+02 pdb=" C2 CTP A1104 " -0.058 2.00e-02 2.50e+03 pdb=" C4 CTP A1104 " 0.060 2.00e-02 2.50e+03 pdb=" C5 CTP A1104 " 0.147 2.00e-02 2.50e+03 pdb=" C6 CTP A1104 " -0.236 2.00e-02 2.50e+03 pdb=" N1 CTP A1104 " -0.174 2.00e-02 2.50e+03 pdb=" N3 CTP A1104 " 0.035 2.00e-02 2.50e+03 pdb=" N4 CTP A1104 " 0.005 2.00e-02 2.50e+03 pdb=" O2 CTP A1104 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 708 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C SER A 708 " -0.025 2.00e-02 2.50e+03 pdb=" O SER A 708 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 709 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 20 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 21 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 21 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 21 " -0.020 5.00e-02 4.00e+02 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 12 2.48 - 3.08: 9503 3.08 - 3.69: 19739 3.69 - 4.29: 31430 4.29 - 4.90: 49906 Nonbonded interactions: 110590 Sorted by model distance: nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A1101 " model vdw 1.873 2.170 nonbonded pdb=" OD2 ASP A 549 " pdb="MG MG A1102 " model vdw 1.986 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A1101 " model vdw 2.023 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A1101 " model vdw 2.032 2.170 nonbonded pdb=" O HOH A1201 " pdb=" O HOH A1202 " model vdw 2.233 3.040 ... (remaining 110585 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.009 0.147 14324 Z= 0.513 Angle : 0.715 9.642 19477 Z= 0.465 Chirality : 0.055 0.176 2153 Planarity : 0.004 0.141 2378 Dihedral : 12.125 89.146 5459 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.51 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1632 helix: -0.07 (0.19), residues: 566 sheet: 0.81 (0.26), residues: 357 loop : -0.11 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 366 TYR 0.001 0.000 TYR A 300 PHE 0.001 0.000 PHE A 548 TRP 0.001 0.000 TRP A 8 HIS 0.001 0.000 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.51 (14324) covalent geometry : angle 0.71464 / 0.46 (19477) hydrogen bonds : bond 0.21113 / 14.05 ( 615) hydrogen bonds : angle 6.60319 / 4.63 ( 1739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.7833 (m-40) cc_final: 0.7455 (p0) REVERT: A 733 VAL cc_start: 0.8096 (t) cc_final: 0.7855 (m) REVERT: A 738 PRO cc_start: 0.6644 (Cg_endo) cc_final: 0.6016 (Cg_exo) REVERT: A 815 SER cc_start: 0.8260 (m) cc_final: 0.8041 (p) REVERT: A 908 MET cc_start: 0.7463 (mtm) cc_final: 0.6959 (mmm) REVERT: A 929 TYR cc_start: 0.7118 (m-80) cc_final: 0.5858 (m-80) REVERT: A 976 THR cc_start: 0.8480 (m) cc_final: 0.8271 (p) REVERT: B 1 MET cc_start: -0.1770 (mmm) cc_final: -0.2356 (mmm) REVERT: B 43 SER cc_start: 0.6533 (m) cc_final: 0.6303 (p) REVERT: C 95 MET cc_start: 0.2033 (ttm) cc_final: 0.0520 (ttm) REVERT: C 97 GLU cc_start: 0.6778 (tt0) cc_final: 0.6527 (tt0) REVERT: C 138 MET cc_start: 0.7000 (ttp) cc_final: 0.6608 (ttp) REVERT: C 195 ILE cc_start: 0.7588 (mt) cc_final: 0.7205 (pt) REVERT: C 317 LYS cc_start: 0.8993 (mttt) cc_final: 0.8631 (mmtm) REVERT: C 347 LYS cc_start: 0.6623 (tttp) cc_final: 0.5974 (mtmt) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1320 time to fit residues: 65.6784 Evaluate side-chains 192 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 551 ASN A 839 HIS A 915 ASN C 134 ASN C 409 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.231388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.180424 restraints weight = 16918.550| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.21 r_work: 0.3509 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 14324 Z= 0.321 Angle : 0.796 13.444 19477 Z= 0.424 Chirality : 0.050 0.178 2153 Planarity : 0.006 0.078 2378 Dihedral : 13.778 69.202 2134 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.65 % Allowed : 6.93 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.19), residues: 1632 helix: 0.39 (0.20), residues: 570 sheet: 0.34 (0.26), residues: 385 loop : -0.67 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 259 TYR 0.027 0.003 TYR A 37 PHE 0.038 0.003 PHE A 175 TRP 0.019 0.003 TRP A 470 HIS 0.009 0.002 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00759 / 0.32 (14324) covalent geometry : angle 0.79597 / 0.42 (19477) hydrogen bonds : bond 0.07522 / 5.03 ( 615) hydrogen bonds : angle 5.27222 / 3.67 ( 1739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8519 (ttm170) REVERT: A 706 GLU cc_start: 0.8128 (tt0) cc_final: 0.7686 (mt-10) REVERT: A 788 LYS cc_start: 0.8518 (mptt) cc_final: 0.8121 (mmtt) REVERT: A 908 MET cc_start: 0.8186 (mtm) cc_final: 0.7712 (mmm) REVERT: A 926 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: B 1 MET cc_start: -0.2081 (mmm) cc_final: -0.2568 (mmm) REVERT: B 43 SER cc_start: 0.6869 (m) cc_final: 0.6530 (p) REVERT: C 347 LYS cc_start: 0.6881 (tttp) cc_final: 0.6232 (mtmt) REVERT: C 384 VAL cc_start: 0.7316 (t) cc_final: 0.6362 (m) outliers start: 25 outliers final: 10 residues processed: 210 average time/residue: 0.0999 time to fit residues: 31.2511 Evaluate side-chains 164 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 309 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 413 ASN A 524 GLN A 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.233982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.182754 restraints weight = 17017.222| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.38 r_work: 0.3537 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14324 Z= 0.140 Angle : 0.573 12.095 19477 Z= 0.312 Chirality : 0.043 0.227 2153 Planarity : 0.004 0.045 2378 Dihedral : 13.447 67.946 2134 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.39 % Allowed : 9.17 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1632 helix: 0.87 (0.21), residues: 579 sheet: 0.40 (0.27), residues: 366 loop : -0.59 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.015 0.001 TYR C 89 PHE 0.027 0.001 PHE A 838 TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (14324) covalent geometry : angle 0.57305 / 0.31 (19477) hydrogen bonds : bond 0.05826 / 3.86 ( 615) hydrogen bonds : angle 4.82357 / 3.36 ( 1739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8506 (mptt) cc_final: 0.8164 (mmtt) REVERT: A 853 MET cc_start: 0.6363 (ppp) cc_final: 0.6034 (ppp) REVERT: A 908 MET cc_start: 0.8023 (mtm) cc_final: 0.7570 (mmm) REVERT: A 926 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: B 1 MET cc_start: -0.1927 (mmm) cc_final: -0.2430 (mmm) REVERT: B 43 SER cc_start: 0.6611 (m) cc_final: 0.6250 (p) REVERT: C 347 LYS cc_start: 0.6834 (tttp) cc_final: 0.6196 (mtmt) REVERT: C 384 VAL cc_start: 0.7250 (t) cc_final: 0.6355 (m) outliers start: 21 outliers final: 14 residues processed: 172 average time/residue: 0.1017 time to fit residues: 26.2885 Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 815 SER Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 120 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.233744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.185409 restraints weight = 17114.122| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 2.29 r_work: 0.3554 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14324 Z= 0.154 Angle : 0.582 14.552 19477 Z= 0.310 Chirality : 0.044 0.304 2153 Planarity : 0.004 0.050 2378 Dihedral : 13.274 68.396 2134 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 1.98 % Allowed : 9.11 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1632 helix: 1.02 (0.21), residues: 579 sheet: 0.30 (0.27), residues: 362 loop : -0.66 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 292 TYR 0.016 0.002 TYR C 89 PHE 0.027 0.002 PHE A 838 TRP 0.018 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14324) covalent geometry : angle 0.58217 / 0.31 (19477) hydrogen bonds : bond 0.05326 / 3.53 ( 615) hydrogen bonds : angle 4.70259 / 3.27 ( 1739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8502 (mptt) cc_final: 0.8182 (mmtt) REVERT: A 908 MET cc_start: 0.8028 (mtm) cc_final: 0.7678 (mmm) REVERT: A 926 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: B 1 MET cc_start: -0.2072 (mmm) cc_final: -0.2551 (mmm) REVERT: B 43 SER cc_start: 0.6616 (m) cc_final: 0.6210 (p) REVERT: C 347 LYS cc_start: 0.7040 (tttp) cc_final: 0.6367 (pttt) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 0.0975 time to fit residues: 25.3718 Evaluate side-chains 169 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 142 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN C 415 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.232102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.182024 restraints weight = 17117.815| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 2.23 r_work: 0.3521 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14324 Z= 0.187 Angle : 0.590 12.002 19477 Z= 0.317 Chirality : 0.044 0.260 2153 Planarity : 0.004 0.049 2378 Dihedral : 13.314 67.994 2134 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.11 % Allowed : 9.31 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1632 helix: 1.00 (0.21), residues: 580 sheet: 0.00 (0.26), residues: 379 loop : -0.80 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 744 TYR 0.018 0.002 TYR C 89 PHE 0.025 0.002 PHE A 838 TRP 0.020 0.002 TRP A 470 HIS 0.006 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (14324) covalent geometry : angle 0.58959 / 0.32 (19477) hydrogen bonds : bond 0.05586 / 3.70 ( 615) hydrogen bonds : angle 4.73689 / 3.29 ( 1739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8472 (ttm170) REVERT: A 788 LYS cc_start: 0.8542 (mptt) cc_final: 0.8188 (mmtt) REVERT: A 908 MET cc_start: 0.7884 (mtm) cc_final: 0.7551 (mmm) REVERT: B 1 MET cc_start: -0.2214 (mmm) cc_final: -0.2726 (mmm) REVERT: B 43 SER cc_start: 0.6587 (m) cc_final: 0.6181 (p) REVERT: C 347 LYS cc_start: 0.7080 (tttp) cc_final: 0.6414 (pttt) REVERT: C 384 VAL cc_start: 0.7315 (t) cc_final: 0.6444 (m) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 0.1046 time to fit residues: 27.5613 Evaluate side-chains 163 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 142 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 145 optimal weight: 40.0000 chunk 135 optimal weight: 0.0670 chunk 62 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.233474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183518 restraints weight = 17011.539| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 2.03 r_work: 0.3587 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14324 Z= 0.114 Angle : 0.529 10.402 19477 Z= 0.287 Chirality : 0.042 0.214 2153 Planarity : 0.004 0.046 2378 Dihedral : 13.043 67.327 2134 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 1.45 % Allowed : 10.76 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1632 helix: 1.31 (0.22), residues: 574 sheet: 0.06 (0.26), residues: 377 loop : -0.72 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 292 TYR 0.017 0.001 TYR C 89 PHE 0.024 0.001 PHE A 838 TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (14324) covalent geometry : angle 0.52874 / 0.29 (19477) hydrogen bonds : bond 0.04514 / 2.98 ( 615) hydrogen bonds : angle 4.53475 / 3.15 ( 1739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7249 (ttt) cc_final: 0.6718 (tpp) REVERT: A 671 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7746 (ttp) REVERT: A 788 LYS cc_start: 0.8526 (mptt) cc_final: 0.8139 (mmtt) REVERT: A 908 MET cc_start: 0.7856 (mtm) cc_final: 0.7535 (mmm) REVERT: B 1 MET cc_start: -0.2106 (mmm) cc_final: -0.2637 (mmm) REVERT: B 43 SER cc_start: 0.6569 (m) cc_final: 0.6108 (p) REVERT: C 87 PHE cc_start: 0.6967 (m-10) cc_final: 0.6655 (m-10) REVERT: C 347 LYS cc_start: 0.7099 (tttp) cc_final: 0.6416 (pttt) outliers start: 22 outliers final: 11 residues processed: 172 average time/residue: 0.1035 time to fit residues: 26.2375 Evaluate side-chains 163 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 127 optimal weight: 8.9990 chunk 154 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.233412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183368 restraints weight = 17017.097| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.25 r_work: 0.3535 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14324 Z= 0.135 Angle : 0.548 16.714 19477 Z= 0.294 Chirality : 0.042 0.213 2153 Planarity : 0.004 0.042 2378 Dihedral : 12.879 67.715 2134 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.45 % Allowed : 11.22 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1632 helix: 1.33 (0.22), residues: 574 sheet: 0.06 (0.26), residues: 369 loop : -0.75 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 292 TYR 0.015 0.001 TYR A 637 PHE 0.036 0.001 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14324) covalent geometry : angle 0.54786 / 0.29 (19477) hydrogen bonds : bond 0.04712 / 3.11 ( 615) hydrogen bonds : angle 4.57454 / 3.18 ( 1739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7842 (ttm) REVERT: A 695 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8399 (mt) REVERT: A 711 MET cc_start: 0.6979 (ppp) cc_final: 0.6681 (ppp) REVERT: A 788 LYS cc_start: 0.8576 (mptt) cc_final: 0.8197 (mmtt) REVERT: A 908 MET cc_start: 0.7827 (mtm) cc_final: 0.7510 (mmm) REVERT: B 1 MET cc_start: -0.2053 (mmm) cc_final: -0.2616 (mmm) REVERT: B 43 SER cc_start: 0.6555 (m) cc_final: 0.6102 (p) REVERT: C 87 PHE cc_start: 0.7093 (m-10) cc_final: 0.6881 (m-10) REVERT: C 347 LYS cc_start: 0.7020 (tttp) cc_final: 0.6280 (pttt) outliers start: 22 outliers final: 17 residues processed: 167 average time/residue: 0.0996 time to fit residues: 24.9532 Evaluate side-chains 170 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.0060 chunk 122 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 40.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.232404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.183112 restraints weight = 16980.484| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 2.14 r_work: 0.3530 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14324 Z= 0.149 Angle : 0.563 15.569 19477 Z= 0.302 Chirality : 0.043 0.251 2153 Planarity : 0.004 0.042 2378 Dihedral : 12.877 67.271 2134 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 2.05 % Allowed : 10.83 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1632 helix: 1.27 (0.22), residues: 575 sheet: 0.02 (0.26), residues: 370 loop : -0.79 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 292 TYR 0.015 0.001 TYR A 637 PHE 0.031 0.002 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14324) covalent geometry : angle 0.56334 / 0.30 (19477) hydrogen bonds : bond 0.04815 / 3.17 ( 615) hydrogen bonds : angle 4.61070 / 3.20 ( 1739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (ttm) REVERT: A 695 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8408 (mt) REVERT: A 788 LYS cc_start: 0.8583 (mptt) cc_final: 0.8208 (mmtt) REVERT: A 908 MET cc_start: 0.7807 (mtm) cc_final: 0.7470 (mmm) REVERT: B 1 MET cc_start: -0.2086 (mmm) cc_final: -0.2636 (mmm) REVERT: C 347 LYS cc_start: 0.7045 (tttp) cc_final: 0.6320 (pttt) outliers start: 31 outliers final: 23 residues processed: 161 average time/residue: 0.1074 time to fit residues: 26.1202 Evaluate side-chains 167 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 318 GLN Chi-restraints excluded: chain C residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 110 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 62 optimal weight: 0.1980 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN B 133 HIS B 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.231683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.182343 restraints weight = 17132.665| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.15 r_work: 0.3527 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14324 Z= 0.167 Angle : 0.577 15.560 19477 Z= 0.309 Chirality : 0.044 0.277 2153 Planarity : 0.004 0.042 2378 Dihedral : 12.926 67.191 2134 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 1.98 % Allowed : 10.89 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1632 helix: 1.18 (0.21), residues: 585 sheet: -0.04 (0.26), residues: 369 loop : -0.78 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.014 0.002 TYR A 637 PHE 0.029 0.002 PHE A 838 TRP 0.016 0.002 TRP A 470 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (14324) covalent geometry : angle 0.57690 / 0.31 (19477) hydrogen bonds : bond 0.05012 / 3.31 ( 615) hydrogen bonds : angle 4.63908 / 3.23 ( 1739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7469 (ttt) cc_final: 0.6963 (ttt) REVERT: A 695 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 788 LYS cc_start: 0.8602 (mptt) cc_final: 0.8235 (mmtt) REVERT: A 908 MET cc_start: 0.7798 (mtm) cc_final: 0.7462 (mmm) REVERT: B 1 MET cc_start: -0.2056 (mmm) cc_final: -0.2626 (mmm) REVERT: C 347 LYS cc_start: 0.7091 (tttp) cc_final: 0.6378 (pttt) REVERT: C 384 VAL cc_start: 0.7218 (t) cc_final: 0.6362 (m) outliers start: 30 outliers final: 26 residues processed: 157 average time/residue: 0.1172 time to fit residues: 27.5712 Evaluate side-chains 165 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 110 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 85 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 103 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 917 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.235258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.184828 restraints weight = 17060.578| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.10 r_work: 0.3598 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14324 Z= 0.104 Angle : 0.525 15.477 19477 Z= 0.283 Chirality : 0.042 0.285 2153 Planarity : 0.004 0.057 2378 Dihedral : 12.562 66.228 2134 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 1.25 % Allowed : 11.62 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1632 helix: 1.47 (0.22), residues: 576 sheet: 0.10 (0.26), residues: 369 loop : -0.65 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.012 0.001 TYR C 199 PHE 0.036 0.001 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.002 0.000 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (14324) covalent geometry : angle 0.52481 / 0.28 (19477) hydrogen bonds : bond 0.03940 / 2.59 ( 615) hydrogen bonds : angle 4.44983 / 3.10 ( 1739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 SER cc_start: 0.8907 (p) cc_final: 0.8583 (m) REVERT: A 671 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: A 788 LYS cc_start: 0.8693 (mptt) cc_final: 0.8342 (mmtt) REVERT: A 908 MET cc_start: 0.7826 (mtm) cc_final: 0.7573 (mmm) REVERT: B 1 MET cc_start: -0.1790 (mmm) cc_final: -0.2416 (mmm) REVERT: C 347 LYS cc_start: 0.6988 (tttp) cc_final: 0.6267 (pttt) outliers start: 19 outliers final: 13 residues processed: 160 average time/residue: 0.1153 time to fit residues: 27.6570 Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 671 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 149 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.233039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.184038 restraints weight = 17078.690| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.20 r_work: 0.3545 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14324 Z= 0.139 Angle : 0.546 16.137 19477 Z= 0.293 Chirality : 0.043 0.251 2153 Planarity : 0.004 0.054 2378 Dihedral : 12.586 67.084 2134 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.06 % Allowed : 12.15 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1632 helix: 1.40 (0.22), residues: 578 sheet: 0.09 (0.27), residues: 364 loop : -0.75 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 636 TYR 0.013 0.001 TYR A 637 PHE 0.032 0.002 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (14324) covalent geometry : angle 0.54567 / 0.29 (19477) hydrogen bonds : bond 0.04503 / 2.97 ( 615) hydrogen bonds : angle 4.50119 / 3.14 ( 1739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.40 seconds wall clock time: 58 minutes 46.60 seconds (3526.60 seconds total)