Starting phenix.real_space_refine on Thu Jun 12 14:36:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8u_36962/06_2025/8k8u_36962.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8u_36962/06_2025/8k8u_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_36962/06_2025/8k8u_36962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8u_36962/06_2025/8k8u_36962.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8u_36962/06_2025/8k8u_36962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8u_36962/06_2025/8k8u_36962.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 chiralities: 1 Time building chain proxies: 8.08, per 1000 atoms: 0.58 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: 3.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.39 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: 5.08 Time building geometry restraints manager: 4.21 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=" 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=" N PRO A 555 " pdb=" CD PRO A 555 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.89e+00 bond pdb=" N PRO A 52 " pdb=" CD PRO A 52 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 6.85e+00 ... (remaining 14319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 18300 1.28 - 2.57: 997 2.57 - 3.85: 141 3.85 - 5.13: 27 5.13 - 6.42: 12 Bond angle restraints: 19477 Sorted by residual: angle pdb=" C ASP B 205 " pdb=" N ASN B 206 " pdb=" CA ASN B 206 " ideal model delta sigma weight residual 122.34 127.51 -5.17 1.39e+00 5.18e-01 1.38e+01 angle pdb=" C ILE A 623 " pdb=" CA ILE A 623 " pdb=" CB ILE A 623 " ideal model delta sigma weight residual 114.00 109.30 4.70 1.31e+00 5.83e-01 1.29e+01 angle pdb=" N GLY C 312 " pdb=" CA GLY C 312 " pdb=" C GLY C 312 " ideal model delta sigma weight residual 112.25 117.05 -4.80 1.34e+00 5.57e-01 1.28e+01 angle pdb=" C PHE A 164 " pdb=" N LEU A 165 " pdb=" CA LEU A 165 " ideal model delta sigma weight residual 122.29 116.60 5.69 1.65e+00 3.67e-01 1.19e+01 angle pdb=" N PRO C 73 " pdb=" CA PRO C 73 " pdb=" C PRO C 73 " ideal model delta sigma weight residual 111.22 115.91 -4.69 1.40e+00 5.10e-01 1.12e+01 ... (remaining 19472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 8260 23.82 - 47.65: 238 47.65 - 71.47: 76 71.47 - 95.30: 6 95.30 - 119.12: 1 Dihedral angle restraints: 8581 sinusoidal: 3710 harmonic: 4871 Sorted by residual: dihedral pdb=" O3B CTP A1104 " pdb=" O3A CTP A1104 " pdb=" PB CTP A1104 " pdb=" PA CTP A1104 " ideal model delta sinusoidal sigma weight residual -39.29 79.82 -119.12 1 2.00e+01 2.50e-03 3.57e+01 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 ... (remaining 8578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1395 0.035 - 0.070: 326 0.070 - 0.106: 245 0.106 - 0.141: 135 0.141 - 0.176: 52 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=" CA VAL A 360 " pdb=" N VAL A 360 " pdb=" C VAL A 360 " pdb=" CB VAL A 360 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 2150 not shown) Planarity restraints: 2379 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C LEU A 424 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO A 425 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 425 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 425 " -0.019 5.00e-02 4.00e+02 ... (remaining 2376 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: 1.090 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 0.051 14324 Z= 0.483 Angle : 0.681 6.417 19477 Z= 0.434 Chirality : 0.054 0.176 2153 Planarity : 0.003 0.035 2379 Dihedral : 12.043 119.119 5439 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.001 0.000 TRP A 8 HIS 0.001 0.000 HIS A 185 PHE 0.001 0.000 PHE A 548 TYR 0.001 0.000 TYR A 300 ARG 0.001 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.21113 ( 615) hydrogen bonds : angle 6.60319 ( 1739) covalent geometry : bond 0.00894 (14324) covalent geometry : angle 0.68077 (19477) *********************** 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 : 1.563 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: 0.8040 (p) REVERT: A 908 MET cc_start: 0.7463 (mtm) cc_final: 0.6959 (mmm) REVERT: A 976 THR cc_start: 0.8480 (m) cc_final: 0.8274 (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: 0.6304 (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: 0.3672 time to fit residues: 179.3952 Evaluate side-chains 191 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 551 ASN A 797 ASN A 839 HIS A 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.239291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188867 restraints weight = 17065.935| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.34 r_work: 0.3634 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14324 Z= 0.144 Angle : 0.587 11.445 19477 Z= 0.315 Chirality : 0.043 0.168 2153 Planarity : 0.004 0.041 2379 Dihedral : 12.826 114.773 2114 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.21 % Favored : 97.73 % Rotamer: Outliers : 1.12 % Allowed : 6.67 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1632 helix: 0.99 (0.21), residues: 572 sheet: 0.69 (0.26), residues: 383 loop : -0.20 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.029 0.002 PHE A 175 TYR 0.015 0.002 TYR C 89 ARG 0.003 0.001 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 615) hydrogen bonds : angle 4.74372 ( 1739) covalent geometry : bond 0.00315 (14324) covalent geometry : angle 0.58652 (19477) *********************** 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 226 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 LYS cc_start: 0.8516 (mptt) cc_final: 0.8286 (mmtm) REVERT: A 908 MET cc_start: 0.7878 (mtm) cc_final: 0.7426 (mmm) REVERT: A 972 PHE cc_start: 0.7300 (m-10) cc_final: 0.7092 (m-10) REVERT: B 1 MET cc_start: -0.1912 (mmm) cc_final: -0.2419 (mmm) REVERT: B 43 SER cc_start: 0.6508 (m) cc_final: 0.6189 (p) REVERT: C 152 PHE cc_start: 0.4263 (m-10) cc_final: 0.4017 (m-10) REVERT: C 347 LYS cc_start: 0.6835 (tttp) cc_final: 0.6156 (mtmm) outliers start: 17 outliers final: 8 residues processed: 218 average time/residue: 0.2747 time to fit residues: 87.6422 Evaluate side-chains 166 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 261 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 226 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 825 ASN A 915 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.231721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181177 restraints weight = 16982.214| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.26 r_work: 0.3524 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14324 Z= 0.212 Angle : 0.624 13.154 19477 Z= 0.332 Chirality : 0.044 0.196 2153 Planarity : 0.005 0.054 2379 Dihedral : 13.067 110.230 2114 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 2.11 % Allowed : 8.51 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1632 helix: 0.93 (0.21), residues: 584 sheet: 0.43 (0.26), residues: 388 loop : -0.57 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 470 HIS 0.006 0.001 HIS A 36 PHE 0.023 0.002 PHE A 838 TYR 0.025 0.002 TYR A 37 ARG 0.005 0.001 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.06015 ( 615) hydrogen bonds : angle 4.81863 ( 1739) covalent geometry : bond 0.00502 (14324) covalent geometry : angle 0.62420 (19477) *********************** 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 203 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 446 ASP cc_start: 0.7336 (t0) cc_final: 0.7126 (t0) REVERT: A 604 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8482 (ttm170) REVERT: A 788 LYS cc_start: 0.8560 (mptt) cc_final: 0.8208 (mmtt) REVERT: A 908 MET cc_start: 0.8094 (mtm) cc_final: 0.7648 (mmm) REVERT: B 1 MET cc_start: -0.2197 (mmm) cc_final: -0.2648 (mmm) REVERT: B 43 SER cc_start: 0.6730 (m) cc_final: 0.6390 (p) REVERT: C 347 LYS cc_start: 0.7115 (tttp) cc_final: 0.6266 (ptpt) outliers start: 32 outliers final: 21 residues processed: 188 average time/residue: 0.2619 time to fit residues: 72.4608 Evaluate side-chains 170 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 352 ASN Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 552 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 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 57 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 128 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 225 GLN A 915 ASN A 917 ASN C 415 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.232742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.183848 restraints weight = 16988.691| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.17 r_work: 0.3559 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14324 Z= 0.139 Angle : 0.528 9.197 19477 Z= 0.284 Chirality : 0.042 0.207 2153 Planarity : 0.004 0.046 2379 Dihedral : 12.707 102.242 2114 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.98 % Allowed : 9.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1632 helix: 1.18 (0.21), residues: 584 sheet: 0.35 (0.26), residues: 386 loop : -0.59 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 470 HIS 0.004 0.001 HIS A 36 PHE 0.023 0.001 PHE A 838 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 615) hydrogen bonds : angle 4.51010 ( 1739) covalent geometry : bond 0.00316 (14324) covalent geometry : angle 0.52820 (19477) *********************** 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 204 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7483 (ttt) cc_final: 0.7022 (ttt) REVERT: A 788 LYS cc_start: 0.8561 (mptt) cc_final: 0.8224 (mmtt) REVERT: A 908 MET cc_start: 0.8024 (mtm) cc_final: 0.7615 (mmm) REVERT: B 1 MET cc_start: -0.2310 (mmm) cc_final: -0.2756 (mmm) REVERT: B 43 SER cc_start: 0.6767 (m) cc_final: 0.6337 (p) REVERT: C 347 LYS cc_start: 0.7142 (tttp) cc_final: 0.6424 (mtmt) outliers start: 30 outliers final: 18 residues processed: 187 average time/residue: 0.2554 time to fit residues: 71.2051 Evaluate side-chains 166 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 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 438 ILE 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 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR 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 2 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 155 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.235028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.184127 restraints weight = 17284.486| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.19 r_work: 0.3569 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4532 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= 0.115 Angle : 0.513 14.400 19477 Z= 0.273 Chirality : 0.041 0.194 2153 Planarity : 0.004 0.045 2379 Dihedral : 12.390 95.337 2114 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 1.58 % Allowed : 10.50 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1632 helix: 1.38 (0.22), residues: 582 sheet: 0.39 (0.26), residues: 379 loop : -0.61 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 PHE 0.022 0.001 PHE A 838 TYR 0.013 0.001 TYR A 637 ARG 0.002 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 615) hydrogen bonds : angle 4.34221 ( 1739) covalent geometry : bond 0.00254 (14324) covalent geometry : angle 0.51307 (19477) *********************** 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 182 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7384 (ttt) cc_final: 0.7064 (ttt) REVERT: A 225 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8484 (mp10) REVERT: A 428 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 788 LYS cc_start: 0.8539 (mptt) cc_final: 0.8198 (mmtt) REVERT: A 908 MET cc_start: 0.7790 (mtm) cc_final: 0.7399 (mmm) REVERT: B 1 MET cc_start: -0.1997 (mmm) cc_final: -0.2526 (mmm) REVERT: B 43 SER cc_start: 0.6526 (m) cc_final: 0.6103 (p) REVERT: C 347 LYS cc_start: 0.6945 (tttp) cc_final: 0.6165 (ptpt) outliers start: 24 outliers final: 16 residues processed: 170 average time/residue: 0.3366 time to fit residues: 87.5695 Evaluate side-chains 163 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 225 GLN 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 549 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN C 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.233984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.184403 restraints weight = 17364.669| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.15 r_work: 0.3557 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14324 Z= 0.126 Angle : 0.521 15.623 19477 Z= 0.277 Chirality : 0.042 0.184 2153 Planarity : 0.004 0.041 2379 Dihedral : 12.384 92.870 2114 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 10.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1632 helix: 1.44 (0.22), residues: 582 sheet: 0.26 (0.26), residues: 387 loop : -0.61 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.003 0.001 HIS A 36 PHE 0.031 0.001 PHE A 175 TYR 0.013 0.001 TYR A 637 ARG 0.002 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 615) hydrogen bonds : angle 4.34516 ( 1739) covalent geometry : bond 0.00283 (14324) covalent geometry : angle 0.52095 (19477) *********************** 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 182 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7468 (ttt) cc_final: 0.6822 (ttt) REVERT: A 428 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7510 (tp) REVERT: A 742 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7405 (ttt-90) REVERT: A 788 LYS cc_start: 0.8567 (mptt) cc_final: 0.8190 (mmtt) REVERT: A 908 MET cc_start: 0.7879 (mtm) cc_final: 0.7509 (mmm) REVERT: B 1 MET cc_start: -0.2236 (mmm) cc_final: -0.2774 (mmm) REVERT: B 43 SER cc_start: 0.6696 (m) cc_final: 0.6256 (p) REVERT: C 347 LYS cc_start: 0.7006 (tttp) cc_final: 0.6226 (ptpt) outliers start: 29 outliers final: 20 residues processed: 171 average time/residue: 0.2793 time to fit residues: 71.4666 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 : 1.562 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 549 ASP 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 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 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 83 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 78 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.230663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180287 restraints weight = 17095.572| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.13 r_work: 0.3512 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14324 Z= 0.190 Angle : 0.584 13.840 19477 Z= 0.310 Chirality : 0.044 0.242 2153 Planarity : 0.004 0.044 2379 Dihedral : 12.719 92.090 2114 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % Rotamer: Outliers : 2.11 % Allowed : 10.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1632 helix: 1.16 (0.22), residues: 597 sheet: 0.05 (0.26), residues: 388 loop : -0.73 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 136 HIS 0.014 0.002 HIS C 252 PHE 0.029 0.002 PHE A 175 TYR 0.020 0.002 TYR B 121 ARG 0.006 0.000 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 615) hydrogen bonds : angle 4.60889 ( 1739) covalent geometry : bond 0.00452 (14324) covalent geometry : angle 0.58383 (19477) *********************** 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 175 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7616 (tp) REVERT: A 788 LYS cc_start: 0.8611 (mptt) cc_final: 0.8252 (mmtt) REVERT: A 908 MET cc_start: 0.7807 (mtm) cc_final: 0.7419 (mmm) REVERT: B 1 MET cc_start: -0.2042 (mmm) cc_final: -0.2651 (mmm) REVERT: C 87 PHE cc_start: 0.7146 (m-10) cc_final: 0.6674 (m-10) REVERT: C 89 TYR cc_start: 0.4312 (t80) cc_final: 0.4054 (t80) REVERT: C 347 LYS cc_start: 0.6997 (tttp) cc_final: 0.6219 (ptpt) REVERT: C 384 VAL cc_start: 0.7218 (t) cc_final: 0.6372 (m) outliers start: 32 outliers final: 24 residues processed: 160 average time/residue: 0.2785 time to fit residues: 66.4019 Evaluate side-chains 158 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 157 ASP 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 222 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 428 ILE Chi-restraints excluded: chain A residue 549 ASP 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 724 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 57 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR 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 16 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN C 134 ASN ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.232795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.183210 restraints weight = 16977.452| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 2.21 r_work: 0.3538 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14324 Z= 0.129 Angle : 0.521 13.552 19477 Z= 0.278 Chirality : 0.042 0.238 2153 Planarity : 0.004 0.043 2379 Dihedral : 12.406 90.343 2114 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.72 % Allowed : 10.63 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1632 helix: 1.39 (0.22), residues: 594 sheet: 0.10 (0.26), residues: 389 loop : -0.70 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.006 0.001 HIS C 252 PHE 0.026 0.001 PHE A 175 TYR 0.013 0.001 TYR A 637 ARG 0.002 0.000 ARG A 636 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 615) hydrogen bonds : angle 4.38721 ( 1739) covalent geometry : bond 0.00295 (14324) covalent geometry : angle 0.52075 (19477) *********************** 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 168 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 788 LYS cc_start: 0.8552 (mptt) cc_final: 0.8179 (mmtt) REVERT: A 908 MET cc_start: 0.7757 (mtm) cc_final: 0.7351 (mmm) REVERT: B 1 MET cc_start: -0.2032 (mmm) cc_final: -0.2638 (mmm) REVERT: C 87 PHE cc_start: 0.7163 (m-10) cc_final: 0.6689 (m-10) REVERT: C 89 TYR cc_start: 0.4094 (t80) cc_final: 0.3679 (t80) REVERT: C 347 LYS cc_start: 0.6942 (tttp) cc_final: 0.6186 (ptpt) REVERT: C 384 VAL cc_start: 0.7137 (t) cc_final: 0.6294 (m) outliers start: 26 outliers final: 22 residues processed: 155 average time/residue: 0.2984 time to fit residues: 68.6912 Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 222 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 428 ILE Chi-restraints excluded: chain A residue 549 ASP 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 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 Chi-restraints excluded: chain C residue 134 ASN 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 54 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 17 optimal weight: 0.0000 chunk 76 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 88 optimal weight: 0.2980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 896 HIS A 915 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.233348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.184072 restraints weight = 17033.235| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 2.13 r_work: 0.3560 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14324 Z= 0.121 Angle : 0.516 13.346 19477 Z= 0.276 Chirality : 0.042 0.239 2153 Planarity : 0.004 0.042 2379 Dihedral : 12.328 89.290 2114 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 10.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1632 helix: 1.50 (0.22), residues: 583 sheet: 0.12 (0.26), residues: 389 loop : -0.65 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.005 0.001 HIS C 252 PHE 0.023 0.001 PHE A 838 TYR 0.013 0.001 TYR A 637 ARG 0.007 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 615) hydrogen bonds : angle 4.33948 ( 1739) covalent geometry : bond 0.00273 (14324) covalent geometry : angle 0.51620 (19477) *********************** 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 168 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7563 (tp) REVERT: A 742 ARG cc_start: 0.7764 (mtm110) cc_final: 0.7546 (ttt-90) REVERT: A 788 LYS cc_start: 0.8525 (mptt) cc_final: 0.8130 (mmtt) REVERT: A 908 MET cc_start: 0.7722 (mtm) cc_final: 0.7364 (mmm) REVERT: B 1 MET cc_start: -0.1787 (mmm) cc_final: -0.2439 (mmm) REVERT: C 87 PHE cc_start: 0.7028 (m-10) cc_final: 0.6637 (m-10) REVERT: C 89 TYR cc_start: 0.4114 (t80) cc_final: 0.3668 (t80) REVERT: C 347 LYS cc_start: 0.6917 (tttp) cc_final: 0.6172 (ptpt) REVERT: C 384 VAL cc_start: 0.7106 (t) cc_final: 0.6284 (m) outliers start: 23 outliers final: 21 residues processed: 158 average time/residue: 0.2616 time to fit residues: 61.8669 Evaluate side-chains 160 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 222 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 428 ILE 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 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ASN 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 31 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.230143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180742 restraints weight = 16968.302| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.14 r_work: 0.3518 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14324 Z= 0.166 Angle : 0.565 12.769 19477 Z= 0.299 Chirality : 0.043 0.234 2153 Planarity : 0.004 0.042 2379 Dihedral : 12.599 89.424 2114 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.65 % Allowed : 10.96 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1632 helix: 1.29 (0.22), residues: 596 sheet: 0.01 (0.26), residues: 389 loop : -0.71 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 470 HIS 0.004 0.001 HIS C 252 PHE 0.023 0.002 PHE A 838 TYR 0.021 0.002 TYR B 121 ARG 0.007 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 615) hydrogen bonds : angle 4.49475 ( 1739) covalent geometry : bond 0.00393 (14324) covalent geometry : angle 0.56473 (19477) ********************** 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 168 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7524 (ttt) cc_final: 0.6976 (ttt) REVERT: A 428 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7608 (tp) REVERT: A 742 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7446 (ttt-90) REVERT: A 788 LYS cc_start: 0.8577 (mptt) cc_final: 0.8185 (mmtt) REVERT: B 1 MET cc_start: -0.1725 (mmm) cc_final: -0.2416 (mmm) REVERT: C 87 PHE cc_start: 0.7101 (m-10) cc_final: 0.6730 (m-10) REVERT: C 89 TYR cc_start: 0.4043 (t80) cc_final: 0.3654 (t80) REVERT: C 347 LYS cc_start: 0.6941 (tttp) cc_final: 0.6308 (pttt) REVERT: C 384 VAL cc_start: 0.7189 (t) cc_final: 0.6349 (m) outliers start: 25 outliers final: 20 residues processed: 156 average time/residue: 0.3005 time to fit residues: 70.3896 Evaluate side-chains 159 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 222 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 428 ILE 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 824 ILE Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ASN 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 16 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 155 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 0.0000 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.234297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.185971 restraints weight = 17210.204| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.26 r_work: 0.3582 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14324 Z= 0.103 Angle : 0.506 12.560 19477 Z= 0.271 Chirality : 0.041 0.237 2153 Planarity : 0.004 0.040 2379 Dihedral : 12.182 87.759 2114 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.06 % Allowed : 11.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1632 helix: 1.60 (0.22), residues: 583 sheet: 0.16 (0.26), residues: 391 loop : -0.56 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS C 252 PHE 0.023 0.001 PHE A 838 TYR 0.011 0.001 TYR C 199 ARG 0.007 0.000 ARG C 135 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 615) hydrogen bonds : angle 4.23952 ( 1739) covalent geometry : bond 0.00217 (14324) covalent geometry : angle 0.50569 (19477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8268.11 seconds wall clock time: 146 minutes 26.16 seconds (8786.16 seconds total)