Starting phenix.real_space_refine on Fri Jul 3 08:31:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.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/7sim_25144/07_2026/7sim_25144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sim_25144/07_2026/7sim_25144.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 ------------------------------------------------------------------------------- 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= 0.052 sd= 0.225 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 70 5.16 5 C 8386 2.51 5 N 2030 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12826 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 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 chiralities: 2 Chain: "D" 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 chiralities: 2 Chain: "E" 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 149 Unusual residues: {' CA': 4, 'CLR': 5, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 93 Unusual residues: {' CA': 4, 'CLR': 3, 'PO4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12826 At special positions: 0 Unit cell: (100.43, 97.11, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 70 16.00 P 2 15.00 O 2330 8.00 N 2030 7.00 C 8386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " 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 " NAG-ASN " NAG A 901 " - " ASN A 468 " " NAG B 901 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 568.9 milliseconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 51.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.789A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.742A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.554A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.759A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 723 through 746 Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.659A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.553A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.958A pdb=" N ALA A 826 " --> pdb=" O PRO A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.967A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.789A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.819A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.595A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 669 removed outlier: 3.803A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 680 through 703 Processing helix chain 'B' and resid 723 through 746 Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.786A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 3.731A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 826 removed outlier: 3.892A pdb=" N ALA B 826 " --> pdb=" O PRO B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 861 removed outlier: 3.958A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.911A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.935A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.124A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.980A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.920A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 648 hydrogen bonds defined for protein. 1854 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: 2.38 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3944 1.34 - 1.46: 2632 1.46 - 1.58: 6496 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 13156 Sorted by residual: bond pdb=" CG TCR B 902 " pdb=" CD1 TCR B 902 " ideal model delta sigma weight residual 1.364 1.473 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CG TCR A 902 " pdb=" CD1 TCR A 902 " ideal model delta sigma weight residual 1.364 1.472 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O2 PO4 A 903 " pdb=" P PO4 A 903 " ideal model delta sigma weight residual 1.567 1.502 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O2 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 17719 2.81 - 5.61: 160 5.61 - 8.42: 16 8.42 - 11.22: 4 11.22 - 14.03: 1 Bond angle restraints: 17900 Sorted by residual: angle pdb=" CA CYS B 598 " pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " ideal model delta sigma weight residual 114.40 124.06 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " pdb=" CG LEU A 690 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " pdb=" SG CYS A 598 " ideal model delta sigma weight residual 114.40 123.22 -8.82 2.30e+00 1.89e-01 1.47e+01 angle pdb=" N GLY B 219 " pdb=" CA GLY B 219 " pdb=" C GLY B 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.25e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.24e+01 ... (remaining 17895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6879 17.52 - 35.03: 574 35.03 - 52.55: 113 52.55 - 70.06: 16 70.06 - 87.58: 12 Dihedral angle restraints: 7594 sinusoidal: 3048 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS B 358 " pdb=" SG CYS B 358 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual 93.00 34.39 58.61 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual 93.00 46.44 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -126.15 40.15 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 7591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1805 0.071 - 0.142: 208 0.142 - 0.213: 14 0.213 - 0.284: 9 0.284 - 0.355: 8 Chirality restraints: 2044 Sorted by residual: chirality pdb=" C14 CLR B 910 " pdb=" C13 CLR B 910 " pdb=" C15 CLR B 910 " pdb=" C8 CLR B 910 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C14 CLR A 911 " pdb=" C13 CLR A 911 " pdb=" C15 CLR A 911 " pdb=" C8 CLR A 911 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C14 CLR B 908 " pdb=" C13 CLR B 908 " pdb=" C15 CLR B 908 " pdb=" C8 CLR B 908 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2041 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 818 " 0.010 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP A 818 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 818 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 818 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 818 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 818 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 818 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 188 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 187 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 188 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3837 2.82 - 3.34: 12227 3.34 - 3.86: 22254 3.86 - 4.38: 26262 4.38 - 4.90: 43675 Nonbonded interactions: 108255 Sorted by model distance: nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.302 3.040 nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.313 3.040 nonbonded pdb=" O PHE A 351 " pdb=" OG1 THR A 355 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 175 " pdb=" NH2 ARG A 185 " model vdw 2.338 3.120 ... (remaining 108250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 910) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' 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=0.00 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.005 0.109 13184 Z= 0.244 Angle : 0.715 14.030 17966 Z= 0.363 Chirality : 0.052 0.355 2044 Planarity : 0.004 0.043 2204 Dihedral : 13.498 87.577 4600 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.36 (0.20), residues: 1546 helix: 1.10 (0.18), residues: 728 sheet: -0.65 (0.36), residues: 212 loop : -0.37 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 795 TYR 0.024 0.002 TYR A 425 PHE 0.017 0.002 PHE B 788 TRP 0.030 0.002 TRP A 818 HIS 0.006 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (13156) covalent geometry : angle 0.70526 / 0.36 (17900) SS BOND : bond 0.00274 / 0.19 ( 18) SS BOND : angle 1.93461 / 1.29 ( 36) hydrogen bonds : bond 0.14060 / 9.62 ( 648) hydrogen bonds : angle 5.34132 / 3.90 ( 1854) link_BETA1-4 : bond 0.00362 / 0.21 ( 4) link_BETA1-4 : angle 1.18201 / 0.86 ( 12) link_NAG-ASN : bond 0.00273 / 0.19 ( 6) link_NAG-ASN : angle 2.70244 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.342 Fit side-chains REVERT: B 257 GLU cc_start: 0.6822 (tp30) cc_final: 0.6602 (mm-30) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.5503 time to fit residues: 130.4655 Evaluate side-chains 204 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 722 ASN B 312 HIS B 357 ASN B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.180189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.155901 restraints weight = 17102.104| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.82 r_work: 0.3559 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13184 Z= 0.206 Angle : 0.599 9.128 17966 Z= 0.315 Chirality : 0.044 0.170 2044 Planarity : 0.004 0.043 2204 Dihedral : 5.349 57.414 1746 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.11 % Allowed : 7.30 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.40 (0.21), residues: 1546 helix: 1.26 (0.18), residues: 712 sheet: -0.61 (0.36), residues: 210 loop : -0.48 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 185 TYR 0.015 0.002 TYR B 435 PHE 0.019 0.002 PHE B 788 TRP 0.014 0.002 TRP A 742 HIS 0.006 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (13156) covalent geometry : angle 0.58884 / 0.31 (17900) SS BOND : bond 0.00345 / 0.24 ( 18) SS BOND : angle 1.83240 / 1.29 ( 36) hydrogen bonds : bond 0.05752 / 3.84 ( 648) hydrogen bonds : angle 4.70018 / 3.44 ( 1854) link_BETA1-4 : bond 0.00296 / 0.17 ( 4) link_BETA1-4 : angle 1.11697 / 0.76 ( 12) link_NAG-ASN : bond 0.00206 / 0.13 ( 6) link_NAG-ASN : angle 2.47002 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.514 Fit side-chains REVERT: A 227 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7877 (ttp80) REVERT: B 257 GLU cc_start: 0.7538 (tp30) cc_final: 0.7120 (tm-30) REVERT: B 771 MET cc_start: 0.4044 (OUTLIER) cc_final: 0.3636 (mmm) outliers start: 15 outliers final: 10 residues processed: 209 average time/residue: 0.5972 time to fit residues: 136.2629 Evaluate side-chains 211 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 771 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 493 ASN A 722 ASN B 312 HIS B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154973 restraints weight = 17135.719| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.80 r_work: 0.3552 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 13184 Z= 0.211 Angle : 0.595 9.333 17966 Z= 0.312 Chirality : 0.044 0.172 2044 Planarity : 0.004 0.049 2204 Dihedral : 5.408 58.559 1746 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.18 % Allowed : 10.32 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.32 (0.21), residues: 1546 helix: 1.25 (0.18), residues: 714 sheet: -0.90 (0.33), residues: 224 loop : -0.48 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 25 TYR 0.019 0.002 TYR A 435 PHE 0.019 0.002 PHE B 788 TRP 0.014 0.002 TRP A 742 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (13156) covalent geometry : angle 0.58485 / 0.31 (17900) SS BOND : bond 0.00395 / 0.29 ( 18) SS BOND : angle 1.82488 / 1.28 ( 36) hydrogen bonds : bond 0.05585 / 3.72 ( 648) hydrogen bonds : angle 4.58126 / 3.35 ( 1854) link_BETA1-4 : bond 0.00221 / 0.14 ( 4) link_BETA1-4 : angle 1.16868 / 0.79 ( 12) link_NAG-ASN : bond 0.00170 / 0.12 ( 6) link_NAG-ASN : angle 2.42696 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.470 Fit side-chains REVERT: A 257 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6065 (tm-30) REVERT: A 341 LYS cc_start: 0.8161 (mppt) cc_final: 0.7957 (mptt) REVERT: A 516 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7378 (ttpp) REVERT: B 257 GLU cc_start: 0.7591 (tp30) cc_final: 0.7135 (tm-30) REVERT: B 605 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7783 (p90) REVERT: B 767 GLU cc_start: 0.5098 (tp30) cc_final: 0.4835 (tp30) outliers start: 16 outliers final: 8 residues processed: 206 average time/residue: 0.6174 time to fit residues: 138.4643 Evaluate side-chains 210 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 738 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 99 optimal weight: 0.4980 chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 722 ASN B 27 GLN B 179 GLN B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.180852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.156732 restraints weight = 17207.929| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.71 r_work: 0.3576 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13184 Z= 0.141 Angle : 0.545 9.264 17966 Z= 0.283 Chirality : 0.041 0.165 2044 Planarity : 0.004 0.042 2204 Dihedral : 5.169 54.750 1746 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.40 % Allowed : 12.61 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.42 (0.21), residues: 1546 helix: 1.33 (0.18), residues: 726 sheet: -0.79 (0.35), residues: 210 loop : -0.51 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 25 TYR 0.020 0.002 TYR B 435 PHE 0.026 0.001 PHE B 832 TRP 0.011 0.001 TRP A 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (13156) covalent geometry : angle 0.53677 / 0.28 (17900) SS BOND : bond 0.00248 / 0.18 ( 18) SS BOND : angle 1.51619 / 1.08 ( 36) hydrogen bonds : bond 0.05052 / 3.36 ( 648) hydrogen bonds : angle 4.39791 / 3.21 ( 1854) link_BETA1-4 : bond 0.00330 / 0.19 ( 4) link_BETA1-4 : angle 1.02798 / 0.69 ( 12) link_NAG-ASN : bond 0.00169 / 0.11 ( 6) link_NAG-ASN : angle 2.19516 / 1.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.488 Fit side-chains REVERT: A 341 LYS cc_start: 0.8173 (mppt) cc_final: 0.7968 (mptt) REVERT: B 257 GLU cc_start: 0.7579 (tp30) cc_final: 0.7132 (tm-30) outliers start: 19 outliers final: 10 residues processed: 214 average time/residue: 0.5914 time to fit residues: 138.3059 Evaluate side-chains 213 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 822 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 27 GLN B 493 ASN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.179000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.154713 restraints weight = 17157.314| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.75 r_work: 0.3551 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 13184 Z= 0.226 Angle : 0.602 10.788 17966 Z= 0.315 Chirality : 0.044 0.191 2044 Planarity : 0.004 0.066 2204 Dihedral : 5.370 57.857 1746 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.92 % Allowed : 13.94 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.41 (0.20), residues: 1546 helix: 1.44 (0.18), residues: 698 sheet: -0.95 (0.33), residues: 222 loop : -0.50 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 227 TYR 0.021 0.002 TYR B 435 PHE 0.018 0.002 PHE B 788 TRP 0.020 0.002 TRP B 742 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (13156) covalent geometry : angle 0.59129 / 0.31 (17900) SS BOND : bond 0.00374 / 0.26 ( 18) SS BOND : angle 1.77348 / 1.25 ( 36) hydrogen bonds : bond 0.05490 / 3.64 ( 648) hydrogen bonds : angle 4.49198 / 3.28 ( 1854) link_BETA1-4 : bond 0.00228 / 0.13 ( 4) link_BETA1-4 : angle 1.20270 / 0.84 ( 12) link_NAG-ASN : bond 0.00181 / 0.13 ( 6) link_NAG-ASN : angle 2.51627 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.488 Fit side-chains REVERT: A 331 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8177 (ttt90) REVERT: A 341 LYS cc_start: 0.8199 (mppt) cc_final: 0.7934 (mptt) REVERT: B 257 GLU cc_start: 0.7835 (tp30) cc_final: 0.7270 (tm-30) REVERT: B 265 LYS cc_start: 0.8554 (mtpt) cc_final: 0.8334 (mtpm) REVERT: B 605 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7502 (p90) outliers start: 26 outliers final: 19 residues processed: 214 average time/residue: 0.5994 time to fit residues: 139.9930 Evaluate side-chains 223 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 618 LEU Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 129 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 179 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 27 GLN B 359 HIS B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158040 restraints weight = 17015.554| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.73 r_work: 0.3600 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13184 Z= 0.115 Angle : 0.520 10.936 17966 Z= 0.270 Chirality : 0.040 0.181 2044 Planarity : 0.003 0.043 2204 Dihedral : 4.947 53.003 1746 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 14.60 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.51 (0.21), residues: 1546 helix: 1.42 (0.18), residues: 728 sheet: -0.81 (0.35), residues: 210 loop : -0.47 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 227 TYR 0.022 0.001 TYR B 435 PHE 0.009 0.001 PHE A 788 TRP 0.016 0.001 TRP B 742 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (13156) covalent geometry : angle 0.51237 / 0.27 (17900) SS BOND : bond 0.00173 / 0.13 ( 18) SS BOND : angle 1.32883 / 0.95 ( 36) hydrogen bonds : bond 0.04733 / 3.15 ( 648) hydrogen bonds : angle 4.24529 / 3.11 ( 1854) link_BETA1-4 : bond 0.00367 / 0.23 ( 4) link_BETA1-4 : angle 0.94393 / 0.62 ( 12) link_NAG-ASN : bond 0.00186 / 0.12 ( 6) link_NAG-ASN : angle 2.05076 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.469 Fit side-chains REVERT: A 227 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7282 (ttm-80) REVERT: A 257 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6186 (tm-30) REVERT: A 270 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8074 (t80) REVERT: A 475 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: B 257 GLU cc_start: 0.7842 (tp30) cc_final: 0.7291 (tm-30) REVERT: B 265 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8283 (mtpm) REVERT: B 270 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8070 (t80) REVERT: B 818 TRP cc_start: 0.8331 (m100) cc_final: 0.8039 (m100) outliers start: 27 outliers final: 13 residues processed: 210 average time/residue: 0.5076 time to fit residues: 116.8638 Evaluate side-chains 204 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 115 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 3 optimal weight: 0.2980 chunk 95 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155438 restraints weight = 17020.178| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.71 r_work: 0.3559 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13184 Z= 0.208 Angle : 0.592 13.182 17966 Z= 0.308 Chirality : 0.044 0.197 2044 Planarity : 0.004 0.054 2204 Dihedral : 5.201 56.685 1746 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.51 % Allowed : 15.34 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.48 (0.21), residues: 1546 helix: 1.51 (0.18), residues: 708 sheet: -0.94 (0.33), residues: 222 loop : -0.52 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 25 TYR 0.022 0.002 TYR B 435 PHE 0.017 0.002 PHE B 853 TRP 0.020 0.002 TRP B 742 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (13156) covalent geometry : angle 0.58257 / 0.31 (17900) SS BOND : bond 0.00354 / 0.26 ( 18) SS BOND : angle 1.63180 / 1.15 ( 36) hydrogen bonds : bond 0.05321 / 3.54 ( 648) hydrogen bonds : angle 4.37974 / 3.20 ( 1854) link_BETA1-4 : bond 0.00252 / 0.15 ( 4) link_BETA1-4 : angle 1.12185 / 0.78 ( 12) link_NAG-ASN : bond 0.00174 / 0.13 ( 6) link_NAG-ASN : angle 2.39755 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.484 Fit side-chains REVERT: A 270 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 257 GLU cc_start: 0.7548 (tp30) cc_final: 0.7104 (tm-30) REVERT: B 265 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8269 (mtpm) REVERT: B 270 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8120 (t80) REVERT: B 605 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7396 (p90) REVERT: B 818 TRP cc_start: 0.8310 (m100) cc_final: 0.8086 (m100) outliers start: 34 outliers final: 17 residues processed: 209 average time/residue: 0.5806 time to fit residues: 132.5955 Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 152 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 27 GLN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157495 restraints weight = 17117.450| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.78 r_work: 0.3588 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13184 Z= 0.123 Angle : 0.536 12.867 17966 Z= 0.277 Chirality : 0.041 0.191 2044 Planarity : 0.004 0.042 2204 Dihedral : 4.924 54.158 1746 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.14 % Allowed : 15.56 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.53 (0.21), residues: 1546 helix: 1.45 (0.18), residues: 726 sheet: -0.84 (0.33), residues: 222 loop : -0.45 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 227 TYR 0.023 0.001 TYR B 435 PHE 0.017 0.001 PHE B 853 TRP 0.016 0.001 TRP B 742 HIS 0.005 0.001 HIS B 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13156) covalent geometry : angle 0.52900 / 0.28 (17900) SS BOND : bond 0.00193 / 0.14 ( 18) SS BOND : angle 1.31079 / 0.93 ( 36) hydrogen bonds : bond 0.04782 / 3.19 ( 648) hydrogen bonds : angle 4.23771 / 3.11 ( 1854) link_BETA1-4 : bond 0.00318 / 0.19 ( 4) link_BETA1-4 : angle 0.91515 / 0.61 ( 12) link_NAG-ASN : bond 0.00195 / 0.13 ( 6) link_NAG-ASN : angle 2.04388 / 1.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.501 Fit side-chains REVERT: A 257 GLU cc_start: 0.6570 (tm-30) cc_final: 0.5940 (tm-30) REVERT: A 270 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 475 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6878 (mt-10) REVERT: B 257 GLU cc_start: 0.7551 (tp30) cc_final: 0.7103 (tm-30) REVERT: B 265 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8213 (mtpm) REVERT: B 270 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8014 (t80) REVERT: B 776 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6881 (mp) REVERT: B 818 TRP cc_start: 0.8288 (m100) cc_final: 0.7999 (m100) outliers start: 29 outliers final: 17 residues processed: 208 average time/residue: 0.5927 time to fit residues: 134.8593 Evaluate side-chains 212 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.155732 restraints weight = 17059.186| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.79 r_work: 0.3561 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 13184 Z= 0.205 Angle : 0.594 11.445 17966 Z= 0.309 Chirality : 0.043 0.200 2044 Planarity : 0.004 0.058 2204 Dihedral : 5.175 58.633 1746 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.06 % Allowed : 16.08 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.48 (0.21), residues: 1546 helix: 1.52 (0.18), residues: 706 sheet: -0.93 (0.33), residues: 222 loop : -0.53 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 25 TYR 0.024 0.002 TYR B 435 PHE 0.014 0.002 PHE B 853 TRP 0.020 0.002 TRP B 742 HIS 0.006 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (13156) covalent geometry : angle 0.58551 / 0.31 (17900) SS BOND : bond 0.00355 / 0.26 ( 18) SS BOND : angle 1.57490 / 1.11 ( 36) hydrogen bonds : bond 0.05254 / 3.49 ( 648) hydrogen bonds : angle 4.34400 / 3.18 ( 1854) link_BETA1-4 : bond 0.00252 / 0.15 ( 4) link_BETA1-4 : angle 1.10147 / 0.77 ( 12) link_NAG-ASN : bond 0.00182 / 0.13 ( 6) link_NAG-ASN : angle 2.36193 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.520 Fit side-chains REVERT: A 227 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7222 (ttm-80) REVERT: A 270 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 257 GLU cc_start: 0.7547 (tp30) cc_final: 0.7108 (tm-30) REVERT: B 270 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 818 TRP cc_start: 0.8292 (m100) cc_final: 0.8008 (m100) outliers start: 28 outliers final: 18 residues processed: 205 average time/residue: 0.5931 time to fit residues: 132.8092 Evaluate side-chains 211 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156350 restraints weight = 17091.804| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.77 r_work: 0.3567 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13184 Z= 0.151 Angle : 0.556 9.861 17966 Z= 0.289 Chirality : 0.042 0.188 2044 Planarity : 0.004 0.048 2204 Dihedral : 4.966 45.358 1746 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 16.37 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.45 (0.21), residues: 1546 helix: 1.45 (0.18), residues: 722 sheet: -0.91 (0.33), residues: 222 loop : -0.56 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 227 TYR 0.023 0.002 TYR B 435 PHE 0.015 0.001 PHE B 853 TRP 0.017 0.001 TRP B 742 HIS 0.009 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (13156) covalent geometry : angle 0.54813 / 0.29 (17900) SS BOND : bond 0.00259 / 0.19 ( 18) SS BOND : angle 1.44086 / 1.02 ( 36) hydrogen bonds : bond 0.04992 / 3.32 ( 648) hydrogen bonds : angle 4.26714 / 3.13 ( 1854) link_BETA1-4 : bond 0.00295 / 0.18 ( 4) link_BETA1-4 : angle 1.01588 / 0.71 ( 12) link_NAG-ASN : bond 0.00168 / 0.12 ( 6) link_NAG-ASN : angle 2.20946 / 1.26 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.467 Fit side-chains REVERT: A 270 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 331 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8068 (ttt90) REVERT: B 257 GLU cc_start: 0.7571 (tp30) cc_final: 0.7118 (tm-30) REVERT: B 265 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8233 (mtpm) REVERT: B 270 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 818 TRP cc_start: 0.8267 (m100) cc_final: 0.7952 (m100) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.6002 time to fit residues: 130.8164 Evaluate side-chains 209 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.180629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156327 restraints weight = 17056.401| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.77 r_work: 0.3574 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13184 Z= 0.161 Angle : 0.569 13.689 17966 Z= 0.294 Chirality : 0.042 0.189 2044 Planarity : 0.004 0.049 2204 Dihedral : 4.973 45.196 1746 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.99 % Allowed : 16.22 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.43 (0.21), residues: 1546 helix: 1.46 (0.18), residues: 720 sheet: -0.91 (0.33), residues: 222 loop : -0.60 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 227 TYR 0.023 0.002 TYR B 435 PHE 0.014 0.001 PHE B 853 TRP 0.017 0.001 TRP B 742 HIS 0.008 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (13156) covalent geometry : angle 0.56114 / 0.29 (17900) SS BOND : bond 0.00267 / 0.19 ( 18) SS BOND : angle 1.43823 / 1.01 ( 36) hydrogen bonds : bond 0.05022 / 3.35 ( 648) hydrogen bonds : angle 4.28962 / 3.15 ( 1854) link_BETA1-4 : bond 0.00295 / 0.17 ( 4) link_BETA1-4 : angle 1.01424 / 0.70 ( 12) link_NAG-ASN : bond 0.00143 / 0.10 ( 6) link_NAG-ASN : angle 2.19760 / 1.25 ( 18) =============================================================================== Job complete usr+sys time: 4760.18 seconds wall clock time: 81 minutes 52.45 seconds (4912.45 seconds total)