Starting phenix.real_space_refine on Fri Jul 3 11:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8u_36962/07_2026/8k8u_36962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8u_36962/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8u_36962/07_2026/8k8u_36962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8u_36962/07_2026/8k8u_36962.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8u_36962/07_2026/8k8u_36962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8u_36962/07_2026/8k8u_36962.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.78, per 1000 atoms: 0.20 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: 0.86 Conformation dependent library (CDL) restraints added in 573.6 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: 1.36 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: 2.09 Time building geometry restraints manager: 1.20 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: 1.010 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- 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 : 0.714 9.642 19477 Z= 0.464 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 0.71429 / 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 : 0.351 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: 0.1411 time to fit residues: 69.8526 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 : 0.445 ------------------------------------------------------------------------------- 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 A 918 ASN C 134 ASN C 409 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.231048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.179926 restraints weight = 16923.592| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.25 r_work: 0.3518 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 14324 Z= 0.325 Angle : 0.810 12.797 19477 Z= 0.431 Chirality : 0.051 0.185 2153 Planarity : 0.007 0.080 2378 Dihedral : 13.850 69.229 2134 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.19 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: -0.22 (0.19), residues: 1632 helix: 0.33 (0.20), residues: 570 sheet: 0.30 (0.26), residues: 385 loop : -0.71 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 292 TYR 0.029 0.003 TYR A 37 PHE 0.038 0.003 PHE A 175 TRP 0.018 0.003 TRP A 470 HIS 0.012 0.003 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.32 (14324) covalent geometry : angle 0.81027 / 0.43 (19477) hydrogen bonds : bond 0.07430 / 4.97 ( 615) hydrogen bonds : angle 5.28795 / 3.68 ( 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 217 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8546 (ttm170) REVERT: A 788 LYS cc_start: 0.8501 (mptt) cc_final: 0.8094 (mmtt) REVERT: A 908 MET cc_start: 0.8096 (mtm) cc_final: 0.7603 (mmm) REVERT: A 926 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: A 976 THR cc_start: 0.8872 (m) cc_final: 0.8648 (p) REVERT: B 1 MET cc_start: -0.2040 (mmm) cc_final: -0.2536 (mmm) REVERT: B 43 SER cc_start: 0.6824 (m) cc_final: 0.6486 (p) REVERT: C 347 LYS cc_start: 0.6854 (tttp) cc_final: 0.6186 (mtmt) REVERT: C 384 VAL cc_start: 0.7296 (t) cc_final: 0.6373 (m) outliers start: 25 outliers final: 10 residues processed: 208 average time/residue: 0.1136 time to fit residues: 34.7400 Evaluate side-chains 162 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 7.9990 chunk 59 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.233952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.183505 restraints weight = 17022.622| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.40 r_work: 0.3531 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14324 Z= 0.142 Angle : 0.576 11.697 19477 Z= 0.314 Chirality : 0.043 0.223 2153 Planarity : 0.004 0.046 2378 Dihedral : 13.491 67.871 2134 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 9.37 % 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: 0.16 (0.20), residues: 1632 helix: 0.88 (0.21), residues: 579 sheet: 0.34 (0.27), residues: 368 loop : -0.62 (0.22), residues: 685 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 0.00294 / 0.14 (14324) covalent geometry : angle 0.57584 / 0.31 (19477) hydrogen bonds : bond 0.05773 / 3.83 ( 615) hydrogen bonds : angle 4.81357 / 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 179 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8514 (mptt) cc_final: 0.8169 (mmtt) REVERT: A 830 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: A 908 MET cc_start: 0.8025 (mtm) cc_final: 0.7574 (mmm) REVERT: A 926 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: B 1 MET cc_start: -0.1922 (mmm) cc_final: -0.2428 (mmm) REVERT: B 43 SER cc_start: 0.6582 (m) cc_final: 0.6206 (p) REVERT: C 347 LYS cc_start: 0.6836 (tttp) cc_final: 0.6195 (mtmt) REVERT: C 384 VAL cc_start: 0.7314 (t) cc_final: 0.6413 (m) outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.1154 time to fit residues: 29.1549 Evaluate side-chains 155 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 815 SER Chi-restraints excluded: chain A residue 830 GLU 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: 2.9990 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 915 ASN C 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.229901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179082 restraints weight = 17038.255| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.28 r_work: 0.3482 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14324 Z= 0.265 Angle : 0.679 14.310 19477 Z= 0.360 Chirality : 0.048 0.280 2153 Planarity : 0.005 0.068 2378 Dihedral : 13.659 68.824 2134 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.24 % Allowed : 9.44 % Favored : 88.32 % 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: 0.68 (0.21), residues: 582 sheet: -0.07 (0.26), residues: 382 loop : -0.86 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 927 TYR 0.023 0.002 TYR A 37 PHE 0.027 0.002 PHE A 838 TRP 0.023 0.002 TRP A 470 HIS 0.008 0.002 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.27 (14324) covalent geometry : angle 0.67872 / 0.36 (19477) hydrogen bonds : bond 0.06537 / 4.36 ( 615) hydrogen bonds : angle 4.97277 / 3.46 ( 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 189 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7873 (tp) REVERT: A 538 GLN cc_start: 0.7821 (mt0) cc_final: 0.7477 (mt0) REVERT: A 604 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8525 (ttm170) REVERT: A 788 LYS cc_start: 0.8541 (mptt) cc_final: 0.8167 (mmtt) REVERT: A 830 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 908 MET cc_start: 0.7971 (mtm) cc_final: 0.7583 (mmm) REVERT: A 926 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: B 1 MET cc_start: -0.2164 (mmm) cc_final: -0.2692 (mmm) REVERT: B 43 SER cc_start: 0.6657 (m) cc_final: 0.6300 (p) REVERT: C 347 LYS cc_start: 0.7089 (tttp) cc_final: 0.6195 (ptpt) REVERT: C 384 VAL cc_start: 0.7317 (t) cc_final: 0.6452 (m) outliers start: 34 outliers final: 20 residues processed: 172 average time/residue: 0.1246 time to fit residues: 31.6038 Evaluate side-chains 169 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 428 ILE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 549 ASP 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 752 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain B residue 57 LEU 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: 0.3980 chunk 141 optimal weight: 50.0000 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 142 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.232892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.184846 restraints weight = 17168.546| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.14 r_work: 0.3543 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4236 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= 0.138 Angle : 0.565 11.990 19477 Z= 0.305 Chirality : 0.043 0.247 2153 Planarity : 0.004 0.043 2378 Dihedral : 13.392 67.476 2134 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.24 % Allowed : 9.90 % Favored : 87.85 % 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: 0.03 (0.20), residues: 1632 helix: 1.04 (0.21), residues: 579 sheet: 0.03 (0.27), residues: 362 loop : -0.80 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 292 TYR 0.016 0.001 TYR C 89 PHE 0.028 0.001 PHE A 175 TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (14324) covalent geometry : angle 0.56490 / 0.31 (19477) hydrogen bonds : bond 0.05160 / 3.41 ( 615) hydrogen bonds : angle 4.69803 / 3.27 ( 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: 34 poor density : 157 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8546 (mptt) cc_final: 0.8188 (mmtt) REVERT: A 830 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: A 908 MET cc_start: 0.7945 (mtm) cc_final: 0.7586 (mmm) REVERT: B 1 MET cc_start: -0.2196 (mmm) cc_final: -0.2699 (mmm) REVERT: B 43 SER cc_start: 0.6595 (m) cc_final: 0.6190 (p) REVERT: C 347 LYS cc_start: 0.7117 (tttp) cc_final: 0.6336 (pttt) REVERT: C 384 VAL cc_start: 0.7317 (t) cc_final: 0.6463 (m) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.1107 time to fit residues: 29.0406 Evaluate side-chains 165 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 735 THR Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 830 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 142 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 30.0000 chunk 135 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.231842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180275 restraints weight = 16867.235| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.15 r_work: 0.3530 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14324 Z= 0.164 Angle : 0.582 11.512 19477 Z= 0.311 Chirality : 0.044 0.236 2153 Planarity : 0.004 0.044 2378 Dihedral : 13.288 67.828 2134 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 2.05 % Allowed : 10.36 % Favored : 87.59 % 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: -0.05 (0.20), residues: 1632 helix: 1.05 (0.21), residues: 582 sheet: -0.07 (0.26), residues: 374 loop : -0.90 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.015 0.002 TYR A 637 PHE 0.024 0.002 PHE A 838 TRP 0.019 0.001 TRP A 470 HIS 0.005 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (14324) covalent geometry : angle 0.58200 / 0.31 (19477) hydrogen bonds : bond 0.05206 / 3.45 ( 615) hydrogen bonds : angle 4.68116 / 3.26 ( 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 177 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 MET cc_start: 0.8896 (ttm) cc_final: 0.8621 (ttm) REVERT: A 788 LYS cc_start: 0.8592 (mptt) cc_final: 0.8218 (mmtt) REVERT: A 807 THR cc_start: 0.8431 (m) cc_final: 0.8222 (m) REVERT: A 908 MET cc_start: 0.7923 (mtm) cc_final: 0.7586 (mmm) REVERT: B 1 MET cc_start: -0.2101 (mmm) cc_final: -0.2647 (mmm) REVERT: B 43 SER cc_start: 0.6619 (m) cc_final: 0.6169 (p) REVERT: C 347 LYS cc_start: 0.7123 (tttp) cc_final: 0.6448 (pttt) REVERT: C 384 VAL cc_start: 0.7325 (t) cc_final: 0.6473 (m) outliers start: 31 outliers final: 21 residues processed: 160 average time/residue: 0.1108 time to fit residues: 26.6409 Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 180 ILE 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 588 LEU 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 752 THR 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: 10.0000 chunk 154 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.232723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.182484 restraints weight = 17015.070| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 2.08 r_work: 0.3550 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14324 Z= 0.131 Angle : 0.546 13.852 19477 Z= 0.293 Chirality : 0.043 0.269 2153 Planarity : 0.004 0.042 2378 Dihedral : 13.106 67.259 2134 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 1.52 % Allowed : 10.96 % Favored : 87.52 % 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: 0.09 (0.20), residues: 1632 helix: 1.25 (0.22), residues: 574 sheet: -0.05 (0.26), residues: 375 loop : -0.84 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.018 0.001 TYR A 928 PHE 0.024 0.001 PHE A 838 TRP 0.017 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14324) covalent geometry : angle 0.54630 / 0.29 (19477) hydrogen bonds : bond 0.04706 / 3.10 ( 615) hydrogen bonds : angle 4.57621 / 3.19 ( 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 173 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 671 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: A 711 MET cc_start: 0.6973 (ppp) cc_final: 0.6687 (ppp) REVERT: A 788 LYS cc_start: 0.8580 (mptt) cc_final: 0.8220 (mmtt) REVERT: A 908 MET cc_start: 0.7910 (mtm) cc_final: 0.7603 (mmm) REVERT: B 1 MET cc_start: -0.2062 (mmm) cc_final: -0.2620 (mmm) REVERT: C 87 PHE cc_start: 0.7062 (m-10) cc_final: 0.6629 (m-10) REVERT: C 347 LYS cc_start: 0.7043 (tttp) cc_final: 0.6317 (pttt) REVERT: C 384 VAL cc_start: 0.7284 (t) cc_final: 0.6470 (m) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.0966 time to fit residues: 23.2002 Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 180 ILE 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 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 824 ILE 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 226 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 133 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 122 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 ASN B 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.232549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.183568 restraints weight = 16991.900| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.16 r_work: 0.3536 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14324 Z= 0.138 Angle : 0.583 18.105 19477 Z= 0.305 Chirality : 0.043 0.241 2153 Planarity : 0.004 0.042 2378 Dihedral : 12.979 67.391 2134 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 1.78 % Allowed : 11.16 % Favored : 87.06 % 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: 0.12 (0.20), residues: 1632 helix: 1.30 (0.22), residues: 574 sheet: -0.05 (0.26), residues: 375 loop : -0.84 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.025 0.001 TYR C 89 PHE 0.039 0.001 PHE A 175 TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS B 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14324) covalent geometry : angle 0.58287 / 0.31 (19477) hydrogen bonds : bond 0.04714 / 3.10 ( 615) hydrogen bonds : angle 4.56053 / 3.16 ( 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 176 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 MET cc_start: 0.6979 (ppp) cc_final: 0.6610 (ppp) REVERT: A 788 LYS cc_start: 0.8596 (mptt) cc_final: 0.8241 (mmtt) REVERT: A 908 MET cc_start: 0.7916 (mtm) cc_final: 0.7642 (mmm) REVERT: B 1 MET cc_start: -0.2090 (mmm) cc_final: -0.2654 (mmm) REVERT: C 347 LYS cc_start: 0.7070 (tttp) cc_final: 0.6366 (pttt) REVERT: C 384 VAL cc_start: 0.7292 (t) cc_final: 0.6451 (m) outliers start: 27 outliers final: 22 residues processed: 164 average time/residue: 0.1080 time to fit residues: 26.6689 Evaluate side-chains 164 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 735 THR Chi-restraints excluded: chain A residue 824 ILE 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 63 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP 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: 7.9990 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.232627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183584 restraints weight = 17184.373| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.19 r_work: 0.3531 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14324 Z= 0.138 Angle : 0.565 15.952 19477 Z= 0.301 Chirality : 0.043 0.266 2153 Planarity : 0.004 0.042 2378 Dihedral : 12.916 67.089 2134 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.85 % Allowed : 11.02 % 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: 1.32 (0.22), residues: 575 sheet: -0.03 (0.26), residues: 369 loop : -0.80 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.014 0.001 TYR A 637 PHE 0.032 0.001 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14324) covalent geometry : angle 0.56460 / 0.30 (19477) hydrogen bonds : bond 0.04633 / 3.06 ( 615) hydrogen bonds : angle 4.56527 / 3.18 ( 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: 28 poor density : 146 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8622 (mptt) cc_final: 0.8274 (mmtt) REVERT: A 908 MET cc_start: 0.7864 (mtm) cc_final: 0.7595 (mmm) REVERT: B 1 MET cc_start: -0.1877 (mmm) cc_final: -0.2452 (mmm) REVERT: C 347 LYS cc_start: 0.7078 (tttp) cc_final: 0.6374 (pttt) REVERT: C 384 VAL cc_start: 0.7287 (t) cc_final: 0.6442 (m) outliers start: 28 outliers final: 26 residues processed: 159 average time/residue: 0.1004 time to fit residues: 24.2543 Evaluate side-chains 166 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 180 ILE 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 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 735 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 63 GLU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 318 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 60 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.0670 chunk 79 optimal weight: 0.6980 chunk 96 optimal weight: 0.0970 chunk 101 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 = 0.232877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.183302 restraints weight = 17068.083| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.28 r_work: 0.3525 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14324 Z= 0.134 Angle : 0.562 16.434 19477 Z= 0.300 Chirality : 0.043 0.265 2153 Planarity : 0.004 0.041 2378 Dihedral : 12.824 66.938 2134 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 1.98 % Allowed : 10.96 % Favored : 87.06 % 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: 1.35 (0.22), residues: 576 sheet: -0.03 (0.26), residues: 369 loop : -0.78 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.013 0.001 TYR A 637 PHE 0.032 0.001 PHE A 175 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14324) covalent geometry : angle 0.56195 / 0.30 (19477) hydrogen bonds : bond 0.04573 / 3.01 ( 615) hydrogen bonds : angle 4.57024 / 3.18 ( 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 171 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8641 (mptt) cc_final: 0.8297 (mmtt) REVERT: A 908 MET cc_start: 0.7766 (mtm) cc_final: 0.7522 (mmm) REVERT: B 1 MET cc_start: -0.1844 (mmm) cc_final: -0.2437 (mmm) REVERT: C 347 LYS cc_start: 0.7071 (tttp) cc_final: 0.6359 (pttt) REVERT: C 384 VAL cc_start: 0.7305 (t) cc_final: 0.6464 (m) outliers start: 30 outliers final: 26 residues processed: 155 average time/residue: 0.0970 time to fit residues: 22.6831 Evaluate side-chains 163 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 180 ILE 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 310 VAL Chi-restraints excluded: chain A residue 340 LYS 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 735 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 149 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.232364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176481 restraints weight = 16910.916| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.90 r_work: 0.3563 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14324 Z= 0.129 Angle : 0.556 15.929 19477 Z= 0.296 Chirality : 0.043 0.269 2153 Planarity : 0.004 0.041 2378 Dihedral : 12.741 66.707 2134 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.91 % Allowed : 11.09 % Favored : 87.00 % 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: 1.37 (0.22), residues: 576 sheet: 0.03 (0.27), residues: 364 loop : -0.77 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.014 0.001 TYR C 61 PHE 0.026 0.001 PHE C 87 TRP 0.016 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14324) covalent geometry : angle 0.55628 / 0.30 (19477) hydrogen bonds : bond 0.04439 / 2.91 ( 615) hydrogen bonds : angle 4.54093 / 3.16 ( 1739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.59 seconds wall clock time: 61 minutes 49.63 seconds (3709.63 seconds total)