Starting phenix.real_space_refine on Thu Feb 5 20:05:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwg_63444/02_2026/9lwg_63444_trim.cif" } resolution = 2.7 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 6298 2.51 5 N 1670 2.21 5 O 1840 1.98 5 H 9222 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19098 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9455 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 575} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, E, F Time building chain proxies: 10.47, per 1000 atoms: 0.55 Number of scatterers: 19098 At special positions: 0 Unit cell: (89.775, 134.235, 98.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 1840 8.00 N 1670 7.00 C 6298 6.00 H 9222 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 409 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 557 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 229 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 409 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 608 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 701 " - " ASN A 431 " " NAG A 702 " - " ASN A 260 " " NAG B 701 " - " ASN B 431 " " NAG B 702 " - " ASN B 260 " " NAG C 1 " - " ASN A 92 " " NAG D 1 " - " ASN A 570 " " NAG E 1 " - " ASN B 92 " " NAG F 1 " - " ASN B 570 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 528.4 milliseconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2248 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 21.6% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 128 through 145 removed outlier: 3.618A pdb=" N LEU A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.871A pdb=" N PHE A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 286' Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.516A pdb=" N LYS A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 365 Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.574A pdb=" N THR A 416 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.870A pdb=" N ARG A 522 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 523 " --> pdb=" O ASN A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 523' Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.948A pdb=" N LEU A 586 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 587 " --> pdb=" O CYS A 584 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 588 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 128 through 145 removed outlier: 3.618A pdb=" N LEU B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 168 through 176 Processing helix chain 'B' and resid 248 through 259 Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.871A pdb=" N PHE B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 281 through 286' Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.516A pdb=" N LYS B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 365 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.574A pdb=" N THR B 416 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 Proline residue: B 464 - end of helix Processing helix chain 'B' and resid 519 through 523 removed outlier: 3.870A pdb=" N ARG B 522 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 523 " --> pdb=" O ASN B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 523' Processing helix chain 'B' and resid 582 through 588 removed outlier: 3.948A pdb=" N LEU B 586 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 587 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 161 removed outlier: 8.621A pdb=" N HIS A 156 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 120 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER A 158 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET A 122 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR A 160 " --> pdb=" O MET A 122 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER A 124 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA A 84 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU A 121 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 86 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU A 123 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 88 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 removed outlier: 4.974A pdb=" N GLY A 186 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 264 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 295 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL A 266 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 240 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR A 267 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 242 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 223 " --> pdb=" O TRP A 241 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N SER A 243 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 369 through 379 removed outlier: 6.238A pdb=" N LEU A 488 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A 375 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A 486 " --> pdb=" O ASP A 375 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS A 377 " --> pdb=" O TRP A 484 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP A 484 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 385 through 390 removed outlier: 6.720A pdb=" N VAL A 424 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 443 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 426 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 439 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 515 removed outlier: 3.672A pdb=" N GLU A 505 " --> pdb=" O PHE A 660 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER A 656 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN A 511 " --> pdb=" O MET A 654 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N MET A 654 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 650 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 536 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 529 Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 68 Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 161 removed outlier: 8.621A pdb=" N HIS B 156 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 120 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER B 158 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET B 122 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 160 " --> pdb=" O MET B 122 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N SER B 124 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 84 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU B 121 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE B 86 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 123 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS B 88 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 221 removed outlier: 4.974A pdb=" N GLY B 186 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 264 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL B 295 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 266 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA B 240 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N TYR B 267 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 242 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 223 " --> pdb=" O TRP B 241 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N SER B 243 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 369 through 379 removed outlier: 6.238A pdb=" N LEU B 488 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP B 375 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR B 486 " --> pdb=" O ASP B 375 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS B 377 " --> pdb=" O TRP B 484 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP B 484 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 385 through 390 removed outlier: 6.720A pdb=" N VAL B 424 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG B 443 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 426 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 439 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 503 through 515 removed outlier: 3.672A pdb=" N GLU B 505 " --> pdb=" O PHE B 660 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER B 656 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASN B 511 " --> pdb=" O MET B 654 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N MET B 654 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 650 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 536 " --> pdb=" O TYR B 661 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 526 through 529 334 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9218 1.03 - 1.23: 130 1.23 - 1.43: 4394 1.43 - 1.62: 5556 1.62 - 1.82: 100 Bond restraints: 19398 Sorted by residual: bond pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ALA A 51 " pdb=" H ALA A 51 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N ALA B 51 " pdb=" H ALA B 51 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N VAL A 558 " pdb=" CA VAL A 558 " ideal model delta sigma weight residual 1.474 1.462 0.012 1.57e-02 4.06e+03 5.97e-01 ... (remaining 19393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 34676 2.16 - 4.33: 128 4.33 - 6.49: 8 6.49 - 8.65: 0 8.65 - 10.81: 2 Bond angle restraints: 34814 Sorted by residual: angle pdb=" CB MET B 626 " pdb=" CG MET B 626 " pdb=" SD MET B 626 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET A 626 " pdb=" CG MET A 626 " pdb=" SD MET A 626 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CG MET B 626 " pdb=" SD MET B 626 " pdb=" CE MET B 626 " ideal model delta sigma weight residual 100.90 105.47 -4.57 2.20e+00 2.07e-01 4.32e+00 angle pdb=" CG MET A 626 " pdb=" SD MET A 626 " pdb=" CE MET A 626 " ideal model delta sigma weight residual 100.90 105.47 -4.57 2.20e+00 2.07e-01 4.32e+00 angle pdb=" C VAL A 588 " pdb=" CA VAL A 588 " pdb=" CB VAL A 588 " ideal model delta sigma weight residual 114.35 112.58 1.77 1.06e+00 8.90e-01 2.78e+00 ... (remaining 34809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8492 17.35 - 34.69: 690 34.69 - 52.04: 240 52.04 - 69.39: 72 69.39 - 86.73: 10 Dihedral angle restraints: 9504 sinusoidal: 5120 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS A 229 " pdb=" SG CYS A 229 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 -39.90 -46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS B 229 " pdb=" SG CYS B 229 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual -86.00 -39.90 -46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA ASP A 609 " pdb=" CB ASP A 609 " pdb=" CG ASP A 609 " pdb=" OD1 ASP A 609 " ideal model delta sinusoidal sigma weight residual -30.00 -84.65 54.65 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 9501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1168 0.040 - 0.079: 196 0.079 - 0.119: 116 0.119 - 0.158: 12 0.158 - 0.198: 2 Chirality restraints: 1494 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 570 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 570 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CA VAL B 506 " pdb=" N VAL B 506 " pdb=" C VAL B 506 " pdb=" CB VAL B 506 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1491 not shown) Planarity restraints: 2936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 463 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.65e-01 pdb=" N PRO A 464 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 463 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.65e-01 pdb=" N PRO B 464 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 61 " 0.014 5.00e-02 4.00e+02 2.17e-02 7.51e-01 pdb=" N PRO B 62 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.012 5.00e-02 4.00e+02 ... (remaining 2933 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1468 2.21 - 2.81: 38824 2.81 - 3.41: 49524 3.41 - 4.00: 69991 4.00 - 4.60: 106505 Nonbonded interactions: 266312 Sorted by model distance: nonbonded pdb=" OD1 ASP A 549 " pdb=" H CYS A 553 " model vdw 1.617 2.450 nonbonded pdb=" OD1 ASP B 549 " pdb=" H CYS B 553 " model vdw 1.617 2.450 nonbonded pdb=" O SER A 175 " pdb="HH12 ARG A 413 " model vdw 1.648 2.450 nonbonded pdb=" O SER B 175 " pdb="HH12 ARG B 413 " model vdw 1.648 2.450 nonbonded pdb="HH22 ARG A 171 " pdb=" O SER B 320 " model vdw 1.659 2.450 ... (remaining 266307 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.500 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: 0.120 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 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 : 0.002 0.033 10206 Z= 0.095 Angle : 0.478 10.813 13932 Z= 0.227 Chirality : 0.041 0.198 1494 Planarity : 0.003 0.023 1778 Dihedral : 15.289 86.732 3826 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.76 % Allowed : 15.27 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.24), residues: 1220 helix: 0.02 (0.38), residues: 210 sheet: -0.15 (0.24), residues: 430 loop : -0.16 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 604 TYR 0.007 0.001 TYR A 267 PHE 0.010 0.001 PHE A 249 TRP 0.003 0.000 TRP B 101 HIS 0.003 0.000 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00218 (10176) covalent geometry : angle 0.47236 (13858) SS BOND : bond 0.00171 ( 16) SS BOND : angle 0.76280 ( 32) hydrogen bonds : bond 0.14755 ( 334) hydrogen bonds : angle 6.84578 ( 894) link_BETA1-4 : bond 0.00385 ( 4) link_BETA1-4 : angle 1.45285 ( 12) link_BETA1-6 : bond 0.00236 ( 2) link_BETA1-6 : angle 1.18856 ( 6) link_NAG-ASN : bond 0.00367 ( 8) link_NAG-ASN : angle 1.20429 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7730 (m-30) cc_final: 0.7344 (m-30) REVERT: A 78 ARG cc_start: 0.5942 (mtm180) cc_final: 0.5405 (mtm180) REVERT: A 134 LEU cc_start: 0.6744 (mt) cc_final: 0.6279 (mt) REVERT: A 138 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 181 HIS cc_start: 0.4858 (m-70) cc_final: 0.4607 (m-70) REVERT: A 196 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7723 (pptt) REVERT: A 277 MET cc_start: 0.6670 (mtp) cc_final: 0.5799 (mtm) REVERT: A 404 ASP cc_start: 0.7128 (t0) cc_final: 0.6800 (t0) REVERT: A 420 TRP cc_start: 0.7703 (m100) cc_final: 0.7471 (m100) REVERT: A 472 SER cc_start: 0.7528 (m) cc_final: 0.7198 (t) REVERT: A 504 PHE cc_start: 0.7851 (p90) cc_final: 0.7506 (p90) REVERT: A 522 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7095 (ptp90) REVERT: B 59 ASP cc_start: 0.7729 (m-30) cc_final: 0.7343 (m-30) REVERT: B 78 ARG cc_start: 0.5942 (mtm180) cc_final: 0.5405 (mtm180) REVERT: B 134 LEU cc_start: 0.6745 (mt) cc_final: 0.6279 (mt) REVERT: B 138 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 181 HIS cc_start: 0.4859 (m-70) cc_final: 0.4607 (m-70) REVERT: B 196 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7722 (pptt) REVERT: B 277 MET cc_start: 0.6670 (mtp) cc_final: 0.5799 (mtm) REVERT: B 404 ASP cc_start: 0.7131 (t0) cc_final: 0.6803 (t0) REVERT: B 420 TRP cc_start: 0.7703 (m100) cc_final: 0.7471 (m100) REVERT: B 472 SER cc_start: 0.7525 (m) cc_final: 0.7196 (t) REVERT: B 504 PHE cc_start: 0.7850 (p90) cc_final: 0.7505 (p90) REVERT: B 522 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7097 (ptp90) outliers start: 8 outliers final: 4 residues processed: 192 average time/residue: 1.1523 time to fit residues: 237.4713 Evaluate side-chains 144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 557 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101759 restraints weight = 36232.769| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.83 r_work: 0.3280 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10206 Z= 0.127 Angle : 0.494 6.375 13932 Z= 0.244 Chirality : 0.042 0.155 1494 Planarity : 0.004 0.051 1778 Dihedral : 5.403 54.940 1624 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.10 % Allowed : 17.56 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.24), residues: 1220 helix: 0.99 (0.36), residues: 216 sheet: 0.09 (0.25), residues: 430 loop : -0.13 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 413 TYR 0.010 0.001 TYR A 341 PHE 0.009 0.001 PHE B 354 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00296 (10176) covalent geometry : angle 0.49023 (13858) SS BOND : bond 0.00703 ( 16) SS BOND : angle 0.54372 ( 32) hydrogen bonds : bond 0.04151 ( 334) hydrogen bonds : angle 5.03791 ( 894) link_BETA1-4 : bond 0.00263 ( 4) link_BETA1-4 : angle 1.28649 ( 12) link_BETA1-6 : bond 0.00421 ( 2) link_BETA1-6 : angle 1.27613 ( 6) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 1.04714 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.443 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8320 (m-30) cc_final: 0.8011 (m-30) REVERT: A 78 ARG cc_start: 0.6308 (mtm180) cc_final: 0.5781 (mtm180) REVERT: A 134 LEU cc_start: 0.7486 (mt) cc_final: 0.7040 (mt) REVERT: A 138 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 196 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7660 (pptt) REVERT: A 225 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7904 (t) REVERT: A 236 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8500 (mmtm) REVERT: A 404 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7571 (t0) REVERT: A 420 TRP cc_start: 0.8176 (m100) cc_final: 0.7891 (m100) REVERT: A 468 ASN cc_start: 0.7911 (t0) cc_final: 0.7347 (m-40) REVERT: A 494 GLN cc_start: 0.8658 (tt0) cc_final: 0.8410 (tt0) REVERT: A 504 PHE cc_start: 0.8246 (p90) cc_final: 0.7387 (p90) REVERT: A 522 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7321 (ptm160) REVERT: B 59 ASP cc_start: 0.8324 (m-30) cc_final: 0.8014 (m-30) REVERT: B 78 ARG cc_start: 0.6319 (mtm180) cc_final: 0.5791 (mtm180) REVERT: B 134 LEU cc_start: 0.7518 (mt) cc_final: 0.7066 (mt) REVERT: B 138 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 196 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7652 (pptt) REVERT: B 225 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7900 (t) REVERT: B 236 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8520 (mmtm) REVERT: B 404 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7575 (t0) REVERT: B 420 TRP cc_start: 0.8185 (m100) cc_final: 0.7900 (m100) REVERT: B 468 ASN cc_start: 0.7895 (t0) cc_final: 0.7331 (m-40) REVERT: B 494 GLN cc_start: 0.8643 (tt0) cc_final: 0.8397 (tt0) REVERT: B 504 PHE cc_start: 0.8241 (p90) cc_final: 0.7373 (p90) REVERT: B 522 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7321 (ptm160) outliers start: 22 outliers final: 6 residues processed: 164 average time/residue: 1.2278 time to fit residues: 214.9431 Evaluate side-chains 150 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 629 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096122 restraints weight = 36840.911| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.84 r_work: 0.3213 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10206 Z= 0.175 Angle : 0.522 6.711 13932 Z= 0.259 Chirality : 0.043 0.152 1494 Planarity : 0.004 0.043 1778 Dihedral : 5.493 55.776 1620 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.10 % Allowed : 17.37 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.24), residues: 1220 helix: 1.06 (0.37), residues: 216 sheet: 0.12 (0.25), residues: 430 loop : -0.25 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 142 TYR 0.013 0.001 TYR A 341 PHE 0.011 0.001 PHE A 448 TRP 0.007 0.001 TRP B 353 HIS 0.004 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00414 (10176) covalent geometry : angle 0.51649 (13858) SS BOND : bond 0.00427 ( 16) SS BOND : angle 0.78352 ( 32) hydrogen bonds : bond 0.03971 ( 334) hydrogen bonds : angle 5.01354 ( 894) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 1.43239 ( 12) link_BETA1-6 : bond 0.00165 ( 2) link_BETA1-6 : angle 1.31749 ( 6) link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 1.28087 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.559 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: symmetry clash REVERT: A 55 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 59 ASP cc_start: 0.8549 (m-30) cc_final: 0.8256 (m-30) REVERT: A 78 ARG cc_start: 0.6327 (mtm180) cc_final: 0.5807 (mtm180) REVERT: A 138 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7379 (mm-30) REVERT: A 196 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7702 (pptt) REVERT: A 225 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8069 (t) REVERT: A 294 MET cc_start: 0.8738 (ttt) cc_final: 0.8450 (ttt) REVERT: A 420 TRP cc_start: 0.8443 (m100) cc_final: 0.8200 (m100) REVERT: A 469 LYS cc_start: 0.7712 (ptmm) cc_final: 0.7196 (mmtt) REVERT: A 494 GLN cc_start: 0.8676 (tt0) cc_final: 0.8459 (tt0) REVERT: A 504 PHE cc_start: 0.8340 (p90) cc_final: 0.7473 (p90) REVERT: B 55 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 59 ASP cc_start: 0.8563 (m-30) cc_final: 0.8272 (m-30) REVERT: B 78 ARG cc_start: 0.6352 (mtm180) cc_final: 0.5831 (mtm180) REVERT: B 138 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7392 (mm-30) REVERT: B 196 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7690 (pptt) REVERT: B 225 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8072 (t) REVERT: B 294 MET cc_start: 0.8740 (ttt) cc_final: 0.8451 (ttt) REVERT: B 420 TRP cc_start: 0.8429 (m100) cc_final: 0.8185 (m100) REVERT: B 469 LYS cc_start: 0.7716 (ptmm) cc_final: 0.7200 (mmtt) REVERT: B 494 GLN cc_start: 0.8678 (tt0) cc_final: 0.8464 (tt0) REVERT: B 504 PHE cc_start: 0.8334 (p90) cc_final: 0.7470 (p90) outliers start: 22 outliers final: 8 residues processed: 156 average time/residue: 1.5485 time to fit residues: 256.4616 Evaluate side-chains 138 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 629 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 114 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 382 ASN B 273 ASN B 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096861 restraints weight = 36747.074| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.85 r_work: 0.3221 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10206 Z= 0.119 Angle : 0.495 6.466 13932 Z= 0.245 Chirality : 0.042 0.150 1494 Planarity : 0.005 0.062 1778 Dihedral : 5.485 55.010 1620 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.53 % Allowed : 17.94 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1220 helix: 1.12 (0.37), residues: 216 sheet: 0.08 (0.25), residues: 430 loop : -0.22 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 522 TYR 0.009 0.001 TYR A 220 PHE 0.010 0.001 PHE B 356 TRP 0.007 0.001 TRP B 353 HIS 0.002 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00284 (10176) covalent geometry : angle 0.48874 (13858) SS BOND : bond 0.00289 ( 16) SS BOND : angle 1.00266 ( 32) hydrogen bonds : bond 0.03405 ( 334) hydrogen bonds : angle 4.84624 ( 894) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 1.36516 ( 12) link_BETA1-6 : bond 0.00330 ( 2) link_BETA1-6 : angle 1.24898 ( 6) link_NAG-ASN : bond 0.00434 ( 8) link_NAG-ASN : angle 1.23863 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 59 ASP cc_start: 0.8531 (m-30) cc_final: 0.8251 (m-30) REVERT: A 78 ARG cc_start: 0.6270 (mtm180) cc_final: 0.5803 (mtm180) REVERT: A 196 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7705 (pptt) REVERT: A 309 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8321 (mtp-110) REVERT: A 420 TRP cc_start: 0.8488 (m100) cc_final: 0.8208 (m100) REVERT: A 469 LYS cc_start: 0.7746 (ptmm) cc_final: 0.7220 (mmtt) REVERT: A 494 GLN cc_start: 0.8658 (tt0) cc_final: 0.8432 (tt0) REVERT: A 504 PHE cc_start: 0.8356 (p90) cc_final: 0.7417 (p90) REVERT: A 522 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7094 (ptp90) REVERT: A 590 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7685 (mtpt) REVERT: B 55 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 59 ASP cc_start: 0.8537 (m-30) cc_final: 0.8262 (m-30) REVERT: B 78 ARG cc_start: 0.6301 (mtm180) cc_final: 0.5828 (mtm180) REVERT: B 138 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7395 (mm-30) REVERT: B 196 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7700 (pptt) REVERT: B 309 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8336 (mtp-110) REVERT: B 420 TRP cc_start: 0.8475 (m100) cc_final: 0.8194 (m100) REVERT: B 469 LYS cc_start: 0.7762 (ptmm) cc_final: 0.7240 (mmtt) REVERT: B 494 GLN cc_start: 0.8652 (tt0) cc_final: 0.8427 (tt0) REVERT: B 504 PHE cc_start: 0.8342 (p90) cc_final: 0.7399 (p90) REVERT: B 522 ARG cc_start: 0.8026 (mtm110) cc_final: 0.7107 (ptp90) REVERT: B 590 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7704 (mtpt) outliers start: 16 outliers final: 8 residues processed: 144 average time/residue: 1.5645 time to fit residues: 238.7452 Evaluate side-chains 135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 614 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094983 restraints weight = 36531.441| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.84 r_work: 0.3198 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10206 Z= 0.145 Angle : 0.511 7.159 13932 Z= 0.253 Chirality : 0.043 0.194 1494 Planarity : 0.004 0.059 1778 Dihedral : 5.781 55.483 1620 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.72 % Allowed : 17.65 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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 (0.24), residues: 1220 helix: 1.09 (0.37), residues: 214 sheet: 0.08 (0.25), residues: 440 loop : -0.19 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 147 TYR 0.011 0.001 TYR B 341 PHE 0.011 0.001 PHE B 356 TRP 0.007 0.001 TRP B 353 HIS 0.002 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00349 (10176) covalent geometry : angle 0.50475 (13858) SS BOND : bond 0.00298 ( 16) SS BOND : angle 1.05594 ( 32) hydrogen bonds : bond 0.03450 ( 334) hydrogen bonds : angle 4.77771 ( 894) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.36817 ( 12) link_BETA1-6 : bond 0.00142 ( 2) link_BETA1-6 : angle 1.28229 ( 6) link_NAG-ASN : bond 0.00423 ( 8) link_NAG-ASN : angle 1.25875 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8559 (m-30) cc_final: 0.8254 (m-30) REVERT: A 78 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5810 (mtm180) REVERT: A 196 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7783 (pptt) REVERT: A 306 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8558 (tp-100) REVERT: A 309 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8336 (mtp-110) REVERT: A 420 TRP cc_start: 0.8560 (m100) cc_final: 0.8317 (m100) REVERT: A 469 LYS cc_start: 0.7791 (ptmm) cc_final: 0.7284 (mmtt) REVERT: A 494 GLN cc_start: 0.8618 (tt0) cc_final: 0.8386 (tt0) REVERT: A 504 PHE cc_start: 0.8384 (p90) cc_final: 0.7463 (p90) REVERT: A 590 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7587 (mtpt) REVERT: B 59 ASP cc_start: 0.8553 (m-30) cc_final: 0.8245 (m-30) REVERT: B 78 ARG cc_start: 0.6296 (mtm180) cc_final: 0.5814 (mtm180) REVERT: B 196 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7786 (pptt) REVERT: B 306 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8555 (tp-100) REVERT: B 309 ARG cc_start: 0.8573 (mmm160) cc_final: 0.8340 (mtp-110) REVERT: B 420 TRP cc_start: 0.8555 (m100) cc_final: 0.8313 (m100) REVERT: B 469 LYS cc_start: 0.7794 (ptmm) cc_final: 0.7292 (mmtt) REVERT: B 494 GLN cc_start: 0.8620 (tt0) cc_final: 0.8394 (tt0) REVERT: B 504 PHE cc_start: 0.8374 (p90) cc_final: 0.7449 (p90) REVERT: B 590 LYS cc_start: 0.7901 (mmmm) cc_final: 0.7628 (mtpt) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 1.5499 time to fit residues: 230.2357 Evaluate side-chains 135 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 629 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095318 restraints weight = 36168.052| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.84 r_work: 0.3203 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10206 Z= 0.111 Angle : 0.493 7.102 13932 Z= 0.243 Chirality : 0.042 0.152 1494 Planarity : 0.004 0.066 1778 Dihedral : 5.669 54.917 1620 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.62 % Allowed : 17.08 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.17 (0.24), residues: 1220 helix: 1.11 (0.37), residues: 216 sheet: 0.09 (0.25), residues: 440 loop : -0.13 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 522 TYR 0.009 0.001 TYR A 220 PHE 0.011 0.001 PHE B 356 TRP 0.007 0.001 TRP B 353 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00269 (10176) covalent geometry : angle 0.48603 (13858) SS BOND : bond 0.00239 ( 16) SS BOND : angle 1.24488 ( 32) hydrogen bonds : bond 0.03169 ( 334) hydrogen bonds : angle 4.62416 ( 894) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 1.31188 ( 12) link_BETA1-6 : bond 0.00306 ( 2) link_BETA1-6 : angle 1.27819 ( 6) link_NAG-ASN : bond 0.00433 ( 8) link_NAG-ASN : angle 1.22362 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8488 (m-30) cc_final: 0.8196 (m-30) REVERT: A 78 ARG cc_start: 0.6247 (mtm180) cc_final: 0.5766 (mtm180) REVERT: A 196 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7808 (pptt) REVERT: A 306 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8576 (tp-100) REVERT: A 309 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8322 (mtp-110) REVERT: A 420 TRP cc_start: 0.8540 (m100) cc_final: 0.8321 (m100) REVERT: A 469 LYS cc_start: 0.7752 (ptmm) cc_final: 0.7292 (mmtt) REVERT: A 494 GLN cc_start: 0.8611 (tt0) cc_final: 0.8365 (tt0) REVERT: A 522 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7008 (ttp80) REVERT: A 590 LYS cc_start: 0.7840 (mmmm) cc_final: 0.7580 (mtpt) REVERT: B 59 ASP cc_start: 0.8496 (m-30) cc_final: 0.8203 (m-30) REVERT: B 78 ARG cc_start: 0.6264 (mtm180) cc_final: 0.5779 (mtm180) REVERT: B 196 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7814 (pptt) REVERT: B 306 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8573 (tp-100) REVERT: B 309 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8336 (mtp-110) REVERT: B 420 TRP cc_start: 0.8540 (m100) cc_final: 0.8319 (m100) REVERT: B 469 LYS cc_start: 0.7757 (ptmm) cc_final: 0.7297 (mmtt) REVERT: B 494 GLN cc_start: 0.8596 (tt0) cc_final: 0.8354 (tt0) REVERT: B 522 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7029 (ttp80) REVERT: B 590 LYS cc_start: 0.7874 (mmmm) cc_final: 0.7613 (mtpt) outliers start: 17 outliers final: 8 residues processed: 134 average time/residue: 1.4028 time to fit residues: 199.4835 Evaluate side-chains 126 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 651 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 16 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093495 restraints weight = 35434.884| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.68 r_work: 0.3119 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10206 Z= 0.128 Angle : 0.493 6.294 13932 Z= 0.244 Chirality : 0.042 0.151 1494 Planarity : 0.004 0.042 1778 Dihedral : 5.689 55.184 1620 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.34 % Allowed : 18.51 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.24), residues: 1220 helix: 1.08 (0.37), residues: 216 sheet: 0.09 (0.25), residues: 440 loop : -0.08 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 522 TYR 0.010 0.001 TYR A 341 PHE 0.011 0.001 PHE A 356 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00308 (10176) covalent geometry : angle 0.48687 (13858) SS BOND : bond 0.00254 ( 16) SS BOND : angle 1.01981 ( 32) hydrogen bonds : bond 0.03212 ( 334) hydrogen bonds : angle 4.59868 ( 894) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 1.32052 ( 12) link_BETA1-6 : bond 0.00287 ( 2) link_BETA1-6 : angle 1.29142 ( 6) link_NAG-ASN : bond 0.00421 ( 8) link_NAG-ASN : angle 1.25101 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8870 (m-30) cc_final: 0.8618 (m-30) REVERT: A 78 ARG cc_start: 0.6658 (mtm180) cc_final: 0.6159 (mtm180) REVERT: A 196 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7818 (pptt) REVERT: A 306 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8673 (tp-100) REVERT: A 469 LYS cc_start: 0.8125 (ptmm) cc_final: 0.7658 (mmtt) REVERT: A 522 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7261 (ttp80) REVERT: A 590 LYS cc_start: 0.8502 (mmmm) cc_final: 0.8280 (mtpt) REVERT: A 641 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: B 59 ASP cc_start: 0.8835 (m-30) cc_final: 0.8590 (m-30) REVERT: B 78 ARG cc_start: 0.6663 (mtm180) cc_final: 0.6164 (mtm180) REVERT: B 196 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7821 (pptt) REVERT: B 306 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8675 (tp-100) REVERT: B 469 LYS cc_start: 0.8124 (ptmm) cc_final: 0.7657 (mmtt) REVERT: B 522 ARG cc_start: 0.8146 (mtm110) cc_final: 0.7257 (ttp80) REVERT: B 590 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8285 (mtpt) REVERT: B 641 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.8044 (mtm-85) outliers start: 14 outliers final: 8 residues processed: 128 average time/residue: 1.5080 time to fit residues: 204.6553 Evaluate side-chains 122 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 651 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090554 restraints weight = 35455.351| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.71 r_work: 0.3076 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10206 Z= 0.186 Angle : 0.547 8.681 13932 Z= 0.272 Chirality : 0.043 0.143 1494 Planarity : 0.004 0.041 1778 Dihedral : 5.980 56.286 1620 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.72 % Allowed : 18.32 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.14 (0.24), residues: 1220 helix: 0.98 (0.37), residues: 212 sheet: 0.07 (0.25), residues: 440 loop : -0.09 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 522 TYR 0.014 0.001 TYR A 220 PHE 0.014 0.002 PHE B 448 TRP 0.007 0.001 TRP B 101 HIS 0.004 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00446 (10176) covalent geometry : angle 0.53961 (13858) SS BOND : bond 0.00334 ( 16) SS BOND : angle 1.26011 ( 32) hydrogen bonds : bond 0.03637 ( 334) hydrogen bonds : angle 4.78348 ( 894) link_BETA1-4 : bond 0.00221 ( 4) link_BETA1-4 : angle 1.51664 ( 12) link_BETA1-6 : bond 0.00121 ( 2) link_BETA1-6 : angle 1.32969 ( 6) link_NAG-ASN : bond 0.00458 ( 8) link_NAG-ASN : angle 1.36495 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.6753 (mtm180) cc_final: 0.6303 (mtm180) REVERT: A 196 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7885 (pptt) REVERT: A 306 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8690 (tp-100) REVERT: A 469 LYS cc_start: 0.8256 (ptmm) cc_final: 0.7856 (mmtt) REVERT: A 535 LYS cc_start: 0.8401 (mttt) cc_final: 0.7979 (mtmm) REVERT: A 590 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8285 (mmtt) REVERT: A 641 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: B 78 ARG cc_start: 0.6759 (mtm180) cc_final: 0.6309 (mtm180) REVERT: B 196 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7890 (pptt) REVERT: B 306 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8683 (tp-100) REVERT: B 469 LYS cc_start: 0.8248 (ptmm) cc_final: 0.7845 (mmtt) REVERT: B 535 LYS cc_start: 0.8388 (mttt) cc_final: 0.7968 (mtmm) REVERT: B 590 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8279 (mmtt) REVERT: B 641 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.8071 (mtm-85) outliers start: 18 outliers final: 10 residues processed: 132 average time/residue: 1.4870 time to fit residues: 207.7564 Evaluate side-chains 118 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 662 GLN Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 662 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092524 restraints weight = 35271.280| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.65 r_work: 0.3105 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10206 Z= 0.109 Angle : 0.502 7.656 13932 Z= 0.248 Chirality : 0.042 0.147 1494 Planarity : 0.004 0.075 1778 Dihedral : 5.816 55.707 1620 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.34 % Allowed : 18.70 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1220 helix: 1.08 (0.37), residues: 212 sheet: 0.08 (0.25), residues: 440 loop : 0.01 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 522 TYR 0.008 0.001 TYR B 341 PHE 0.011 0.001 PHE A 356 TRP 0.007 0.001 TRP B 353 HIS 0.002 0.001 HIS A 181 Details of bonding type rmsd covalent geometry : bond 0.00263 (10176) covalent geometry : angle 0.49566 (13858) SS BOND : bond 0.00250 ( 16) SS BOND : angle 0.99975 ( 32) hydrogen bonds : bond 0.03155 ( 334) hydrogen bonds : angle 4.62574 ( 894) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.36423 ( 12) link_BETA1-6 : bond 0.00201 ( 2) link_BETA1-6 : angle 1.27150 ( 6) link_NAG-ASN : bond 0.00425 ( 8) link_NAG-ASN : angle 1.24967 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8923 (m-30) cc_final: 0.8707 (m-30) REVERT: A 78 ARG cc_start: 0.6727 (mtm180) cc_final: 0.6290 (mtm180) REVERT: A 196 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7869 (pptt) REVERT: A 306 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8694 (tp-100) REVERT: A 469 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7683 (mmtt) REVERT: A 522 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7281 (ttp80) REVERT: A 535 LYS cc_start: 0.8361 (mttt) cc_final: 0.7978 (mtmm) REVERT: A 590 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8249 (mmtt) REVERT: B 59 ASP cc_start: 0.8924 (m-30) cc_final: 0.8680 (m-30) REVERT: B 78 ARG cc_start: 0.6733 (mtm180) cc_final: 0.6292 (mtm180) REVERT: B 196 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7880 (pptt) REVERT: B 306 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8676 (tp-100) REVERT: B 469 LYS cc_start: 0.8143 (ptmm) cc_final: 0.7678 (mmtt) REVERT: B 522 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7268 (ttp80) REVERT: B 535 LYS cc_start: 0.8342 (mttt) cc_final: 0.7962 (mtmm) REVERT: B 590 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8246 (mmtt) outliers start: 14 outliers final: 4 residues processed: 118 average time/residue: 1.5598 time to fit residues: 194.5418 Evaluate side-chains 112 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094109 restraints weight = 35225.908| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.61 r_work: 0.3173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10206 Z= 0.098 Angle : 0.498 10.035 13932 Z= 0.244 Chirality : 0.042 0.154 1494 Planarity : 0.004 0.065 1778 Dihedral : 5.650 54.780 1620 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.95 % Allowed : 18.89 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.25), residues: 1220 helix: 1.09 (0.37), residues: 212 sheet: 0.03 (0.25), residues: 440 loop : 0.11 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 522 TYR 0.009 0.001 TYR B 220 PHE 0.011 0.001 PHE B 356 TRP 0.007 0.001 TRP A 353 HIS 0.007 0.001 HIS B 546 Details of bonding type rmsd covalent geometry : bond 0.00239 (10176) covalent geometry : angle 0.49283 (13858) SS BOND : bond 0.00216 ( 16) SS BOND : angle 0.94014 ( 32) hydrogen bonds : bond 0.02909 ( 334) hydrogen bonds : angle 4.48452 ( 894) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 1.21777 ( 12) link_BETA1-6 : bond 0.00229 ( 2) link_BETA1-6 : angle 1.25319 ( 6) link_NAG-ASN : bond 0.00405 ( 8) link_NAG-ASN : angle 1.20057 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.8871 (m-30) cc_final: 0.8668 (m-30) REVERT: A 78 ARG cc_start: 0.6672 (mtm180) cc_final: 0.6255 (mtm180) REVERT: A 122 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.7702 (mmt) REVERT: A 196 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7839 (pptt) REVERT: A 306 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8661 (tp-100) REVERT: A 469 LYS cc_start: 0.8169 (ptmm) cc_final: 0.7737 (mmtt) REVERT: A 522 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7202 (ttp80) REVERT: A 590 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8233 (mmtt) REVERT: B 59 ASP cc_start: 0.8872 (m-30) cc_final: 0.8672 (m-30) REVERT: B 78 ARG cc_start: 0.6681 (mtm180) cc_final: 0.6261 (mtm180) REVERT: B 122 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.7688 (mmt) REVERT: B 196 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7847 (pptt) REVERT: B 306 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8659 (tp-100) REVERT: B 469 LYS cc_start: 0.8154 (ptmm) cc_final: 0.7716 (mmtt) REVERT: B 522 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7196 (ttp80) REVERT: B 590 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8243 (mmtt) outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 1.7336 time to fit residues: 230.8539 Evaluate side-chains 120 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 557 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS B 380 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093542 restraints weight = 35556.933| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.59 r_work: 0.2998 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10206 Z= 0.114 Angle : 0.502 8.308 13932 Z= 0.246 Chirality : 0.042 0.153 1494 Planarity : 0.004 0.067 1778 Dihedral : 5.704 54.993 1620 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.95 % Allowed : 19.08 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1220 helix: 0.79 (0.36), residues: 224 sheet: 0.07 (0.25), residues: 440 loop : 0.14 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 522 TYR 0.008 0.001 TYR B 341 PHE 0.011 0.001 PHE B 356 TRP 0.007 0.001 TRP A 101 HIS 0.002 0.000 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00277 (10176) covalent geometry : angle 0.49653 (13858) SS BOND : bond 0.00244 ( 16) SS BOND : angle 0.91304 ( 32) hydrogen bonds : bond 0.03017 ( 334) hydrogen bonds : angle 4.48710 ( 894) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 1.24970 ( 12) link_BETA1-6 : bond 0.00223 ( 2) link_BETA1-6 : angle 1.26715 ( 6) link_NAG-ASN : bond 0.00389 ( 8) link_NAG-ASN : angle 1.23207 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6935.71 seconds wall clock time: 117 minutes 57.36 seconds (7077.36 seconds total)