Starting phenix.real_space_refine on Wed Mar 4 11:08:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sim_25144/03_2026/7sim_25144.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sim_25144/03_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_25144/03_2026/7sim_25144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sim_25144/03_2026/7sim_25144.map" model { file = "/net/cci-nas-00/data/ceres_data/7sim_25144/03_2026/7sim_25144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sim_25144/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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: 3.04, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 564.3 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: 0.30 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: 2.18 Time building geometry restraints manager: 1.31 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: 7481 17.52 - 35.03: 601 35.03 - 52.55: 136 52.55 - 70.06: 22 70.06 - 87.58: 12 Dihedral angle restraints: 8252 sinusoidal: 3706 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 8249 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: 0.440 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: 12.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:8.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 13.376 87.577 5258 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 covalent geometry : bond 0.00519 (13156) covalent geometry : angle 0.70526 (17900) SS BOND : bond 0.00274 ( 18) SS BOND : angle 1.93461 ( 36) hydrogen bonds : bond 0.14060 ( 648) hydrogen bonds : angle 5.34132 ( 1854) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.18201 ( 12) link_NAG-ASN : bond 0.00273 ( 6) link_NAG-ASN : angle 2.70244 ( 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 : 0.391 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: 0.6019 time to fit residues: 142.0291 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 : 0.405 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4159 r_free = 0.4159 target = 0.179937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155700 restraints weight = 17100.801| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.77 r_work: 0.3565 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 13184 Z= 0.205 Angle : 0.600 9.114 17966 Z= 0.316 Chirality : 0.044 0.172 2044 Planarity : 0.004 0.043 2204 Dihedral : 6.846 57.754 2404 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.12 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: 0.39 (0.21), residues: 1546 helix: 1.25 (0.18), residues: 712 sheet: -0.63 (0.36), residues: 210 loop : -0.49 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 185 TYR 0.016 0.002 TYR B 435 PHE 0.019 0.002 PHE A 788 TRP 0.013 0.002 TRP A 742 HIS 0.006 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00468 (13156) covalent geometry : angle 0.58963 (17900) SS BOND : bond 0.00351 ( 18) SS BOND : angle 1.83920 ( 36) hydrogen bonds : bond 0.05683 ( 648) hydrogen bonds : angle 4.67925 ( 1854) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 1.23373 ( 12) link_NAG-ASN : bond 0.00212 ( 6) link_NAG-ASN : angle 2.47190 ( 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 225 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.484 Fit side-chains REVERT: A 227 ARG cc_start: 0.8259 (ttp80) cc_final: 0.8020 (ttp80) REVERT: B 257 GLU cc_start: 0.7754 (tp30) cc_final: 0.7223 (tm-30) REVERT: B 771 MET cc_start: 0.4093 (OUTLIER) cc_final: 0.3652 (mmm) outliers start: 15 outliers final: 10 residues processed: 211 average time/residue: 0.5910 time to fit residues: 135.5928 Evaluate side-chains 209 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 0.0060 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 144 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 722 ASN B 357 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.180965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.156600 restraints weight = 17194.801| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.73 r_work: 0.3575 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13184 Z= 0.153 Angle : 0.546 8.211 17966 Z= 0.286 Chirality : 0.042 0.172 2044 Planarity : 0.004 0.042 2204 Dihedral : 6.426 58.763 2404 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.03 % Allowed : 10.32 % Favored : 88.64 % 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: 1.30 (0.18), residues: 728 sheet: -0.73 (0.35), residues: 210 loop : -0.48 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 25 TYR 0.019 0.002 TYR B 435 PHE 0.016 0.001 PHE A 788 TRP 0.013 0.002 TRP A 742 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00343 (13156) covalent geometry : angle 0.53683 (17900) SS BOND : bond 0.00253 ( 18) SS BOND : angle 1.55908 ( 36) hydrogen bonds : bond 0.05220 ( 648) hydrogen bonds : angle 4.45243 ( 1854) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.19663 ( 12) link_NAG-ASN : bond 0.00186 ( 6) link_NAG-ASN : angle 2.27239 ( 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 213 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.328 Fit side-chains REVERT: A 475 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: B 257 GLU cc_start: 0.7602 (tp30) cc_final: 0.7159 (tm-30) REVERT: B 767 GLU cc_start: 0.5075 (tp30) cc_final: 0.4708 (tp30) outliers start: 14 outliers final: 7 residues processed: 200 average time/residue: 0.5790 time to fit residues: 126.3283 Evaluate side-chains 203 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 475 GLU 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 738 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 338 HIS A 357 ASN A 493 ASN A 595 HIS A 722 ASN B 27 GLN B 357 ASN B 493 ASN B 722 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.177959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153397 restraints weight = 17091.285| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.83 r_work: 0.3523 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 13184 Z= 0.304 Angle : 0.669 11.327 17966 Z= 0.351 Chirality : 0.048 0.199 2044 Planarity : 0.005 0.054 2204 Dihedral : 6.511 57.115 2404 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.99 % Allowed : 11.73 % Favored : 86.28 % 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: 0.20 (0.20), residues: 1546 helix: 1.21 (0.18), residues: 698 sheet: -1.03 (0.32), residues: 224 loop : -0.55 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 25 TYR 0.019 0.003 TYR A 425 PHE 0.025 0.002 PHE A 788 TRP 0.015 0.002 TRP A 742 HIS 0.007 0.002 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00702 (13156) covalent geometry : angle 0.65637 (17900) SS BOND : bond 0.00500 ( 18) SS BOND : angle 2.10864 ( 36) hydrogen bonds : bond 0.05977 ( 648) hydrogen bonds : angle 4.69176 ( 1854) link_BETA1-4 : bond 0.00315 ( 4) link_BETA1-4 : angle 1.51777 ( 12) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 2.80096 ( 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 235 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.322 Fit side-chains REVERT: A 265 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8306 (mtpm) REVERT: B 257 GLU cc_start: 0.7594 (tp30) cc_final: 0.7153 (tm-30) REVERT: B 265 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8295 (mtpm) REVERT: B 605 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7501 (p90) outliers start: 27 outliers final: 17 residues processed: 213 average time/residue: 0.5819 time to fit residues: 134.9186 Evaluate side-chains 221 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 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 738 ILE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU 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 669 ILE Chi-restraints excluded: chain B residue 722 ASN 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: 7.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 179 GLN A 338 HIS A 357 ASN A 595 HIS A 722 ASN B 27 GLN B 179 GLN B 357 ASN B 722 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.157462 restraints weight = 17239.067| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.71 r_work: 0.3597 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13184 Z= 0.127 Angle : 0.537 11.489 17966 Z= 0.280 Chirality : 0.041 0.181 2044 Planarity : 0.003 0.043 2204 Dihedral : 6.139 59.683 2404 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.77 % Allowed : 13.79 % Favored : 84.44 % 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: 0.38 (0.21), residues: 1546 helix: 1.30 (0.18), residues: 728 sheet: -0.88 (0.34), residues: 210 loop : -0.53 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 227 TYR 0.022 0.002 TYR A 435 PHE 0.015 0.001 PHE A 762 TRP 0.016 0.001 TRP B 742 HIS 0.006 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00279 (13156) covalent geometry : angle 0.52911 (17900) SS BOND : bond 0.00222 ( 18) SS BOND : angle 1.44865 ( 36) hydrogen bonds : bond 0.04895 ( 648) hydrogen bonds : angle 4.32239 ( 1854) link_BETA1-4 : bond 0.00379 ( 4) link_BETA1-4 : angle 1.11945 ( 12) link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 2.21428 ( 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 227 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.466 Fit side-chains REVERT: A 265 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8322 (mtpm) REVERT: A 270 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8125 (t80) REVERT: A 475 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 257 GLU cc_start: 0.7761 (tp30) cc_final: 0.7208 (tm-30) REVERT: B 265 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8306 (mtpm) REVERT: B 270 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8116 (t80) REVERT: B 475 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: B 818 TRP cc_start: 0.8400 (m100) cc_final: 0.8150 (m100) outliers start: 24 outliers final: 11 residues processed: 214 average time/residue: 0.5596 time to fit residues: 130.5040 Evaluate side-chains 211 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 475 GLU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE 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: 9.9990 chunk 72 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 722 ASN B 27 GLN B 359 HIS B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156533 restraints weight = 16965.471| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.77 r_work: 0.3579 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1760 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= 0.150 Angle : 0.548 12.925 17966 Z= 0.285 Chirality : 0.042 0.184 2044 Planarity : 0.004 0.041 2204 Dihedral : 6.032 59.574 2404 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.77 % Allowed : 14.97 % Favored : 83.26 % 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: 1.42 (0.18), residues: 722 sheet: -0.91 (0.33), residues: 222 loop : -0.55 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 227 TYR 0.021 0.002 TYR B 435 PHE 0.018 0.001 PHE B 788 TRP 0.017 0.001 TRP B 742 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00338 (13156) covalent geometry : angle 0.53959 (17900) SS BOND : bond 0.00267 ( 18) SS BOND : angle 1.45763 ( 36) hydrogen bonds : bond 0.05019 ( 648) hydrogen bonds : angle 4.31327 ( 1854) link_BETA1-4 : bond 0.00304 ( 4) link_BETA1-4 : angle 1.16155 ( 12) link_NAG-ASN : bond 0.00186 ( 6) link_NAG-ASN : angle 2.26467 ( 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 216 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.462 Fit side-chains REVERT: A 257 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6126 (tm-30) REVERT: A 265 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8340 (mtpm) REVERT: A 270 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 516 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7346 (pptt) REVERT: B 257 GLU cc_start: 0.7775 (tp30) cc_final: 0.7241 (tm-30) REVERT: B 265 LYS cc_start: 0.8532 (mtpt) cc_final: 0.8305 (mtpm) REVERT: B 270 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8153 (t80) REVERT: B 818 TRP cc_start: 0.8376 (m100) cc_final: 0.8128 (m100) outliers start: 24 outliers final: 14 residues processed: 202 average time/residue: 0.5639 time to fit residues: 124.5126 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 771 MET 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: 5.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 722 ASN B 27 GLN B 722 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155999 restraints weight = 17049.949| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.75 r_work: 0.3565 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13184 Z= 0.166 Angle : 0.557 11.915 17966 Z= 0.290 Chirality : 0.042 0.199 2044 Planarity : 0.004 0.057 2204 Dihedral : 5.942 59.494 2404 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.29 % Allowed : 15.19 % Favored : 82.52 % 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: 1.42 (0.18), residues: 720 sheet: -0.92 (0.33), residues: 222 loop : -0.56 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 227 TYR 0.023 0.002 TYR A 435 PHE 0.014 0.001 PHE A 788 TRP 0.018 0.002 TRP B 742 HIS 0.004 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00376 (13156) covalent geometry : angle 0.54830 (17900) SS BOND : bond 0.00297 ( 18) SS BOND : angle 1.49989 ( 36) hydrogen bonds : bond 0.05062 ( 648) hydrogen bonds : angle 4.30618 ( 1854) link_BETA1-4 : bond 0.00303 ( 4) link_BETA1-4 : angle 1.19271 ( 12) link_NAG-ASN : bond 0.00190 ( 6) link_NAG-ASN : angle 2.31067 ( 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 219 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.454 Fit side-chains REVERT: A 257 GLU cc_start: 0.6590 (tm-30) cc_final: 0.5946 (tm-30) REVERT: A 270 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8113 (t80) REVERT: A 475 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: B 257 GLU cc_start: 0.7520 (tp30) cc_final: 0.7069 (tm-30) REVERT: B 270 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 475 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: B 818 TRP cc_start: 0.8339 (m100) cc_final: 0.8136 (m100) outliers start: 31 outliers final: 16 residues processed: 204 average time/residue: 0.5674 time to fit residues: 126.0977 Evaluate side-chains 206 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 475 GLU 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 695 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: 0.0970 chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 722 ASN B 27 GLN B 312 HIS B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.181285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157245 restraints weight = 17070.490| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.77 r_work: 0.3586 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13184 Z= 0.140 Angle : 0.548 15.013 17966 Z= 0.282 Chirality : 0.041 0.192 2044 Planarity : 0.004 0.043 2204 Dihedral : 6.100 59.464 2404 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 15.63 % Favored : 82.45 % 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: 1.41 (0.18), residues: 722 sheet: -0.90 (0.33), residues: 222 loop : -0.48 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 25 TYR 0.023 0.002 TYR A 435 PHE 0.011 0.001 PHE A 469 TRP 0.015 0.001 TRP B 742 HIS 0.005 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00313 (13156) covalent geometry : angle 0.54071 (17900) SS BOND : bond 0.00233 ( 18) SS BOND : angle 1.38096 ( 36) hydrogen bonds : bond 0.04932 ( 648) hydrogen bonds : angle 4.26919 ( 1854) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 1.11906 ( 12) link_NAG-ASN : bond 0.00172 ( 6) link_NAG-ASN : angle 2.18945 ( 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 215 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.323 Fit side-chains REVERT: A 257 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6122 (tm-30) REVERT: A 265 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8343 (mtpm) REVERT: A 270 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 331 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8099 (ttt90) REVERT: A 475 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: A 516 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7351 (pptt) REVERT: B 257 GLU cc_start: 0.7840 (tp30) cc_final: 0.7291 (tm-30) REVERT: B 265 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8312 (mtpm) REVERT: B 270 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 475 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: B 818 TRP cc_start: 0.8351 (m100) cc_final: 0.8060 (m100) outliers start: 26 outliers final: 15 residues processed: 202 average time/residue: 0.5836 time to fit residues: 128.3144 Evaluate side-chains 207 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 475 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 738 ILE 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: 10.0000 chunk 105 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 109 optimal weight: 0.0270 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 312 HIS B 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.181670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157599 restraints weight = 17111.437| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.77 r_work: 0.3594 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13184 Z= 0.126 Angle : 0.526 10.168 17966 Z= 0.273 Chirality : 0.041 0.185 2044 Planarity : 0.003 0.041 2204 Dihedral : 5.931 58.706 2404 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.77 % Allowed : 16.22 % Favored : 82.01 % 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: 0.56 (0.21), residues: 1546 helix: 1.50 (0.18), residues: 722 sheet: -0.85 (0.33), residues: 222 loop : -0.45 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 227 TYR 0.023 0.001 TYR A 435 PHE 0.013 0.001 PHE A 788 TRP 0.015 0.001 TRP B 742 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00277 (13156) covalent geometry : angle 0.51840 (17900) SS BOND : bond 0.00203 ( 18) SS BOND : angle 1.29269 ( 36) hydrogen bonds : bond 0.04743 ( 648) hydrogen bonds : angle 4.19090 ( 1854) link_BETA1-4 : bond 0.00330 ( 4) link_BETA1-4 : angle 1.06363 ( 12) link_NAG-ASN : bond 0.00154 ( 6) link_NAG-ASN : angle 2.08539 ( 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 214 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.520 Fit side-chains REVERT: A 257 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6148 (tm-30) REVERT: A 265 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8304 (mtpm) REVERT: A 270 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 516 LYS cc_start: 0.7634 (ttpp) cc_final: 0.7354 (pptt) REVERT: B 257 GLU cc_start: 0.7843 (tp30) cc_final: 0.7300 (tm-30) REVERT: B 265 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8249 (mtpm) REVERT: B 270 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8061 (t80) REVERT: B 475 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: B 818 TRP cc_start: 0.8327 (m100) cc_final: 0.8036 (m100) outliers start: 24 outliers final: 12 residues processed: 203 average time/residue: 0.5617 time to fit residues: 124.1596 Evaluate side-chains 200 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 529 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET 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 475 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS B 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.180278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.156270 restraints weight = 17107.838| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.73 r_work: 0.3567 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1951 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= 0.176 Angle : 0.558 10.348 17966 Z= 0.292 Chirality : 0.042 0.196 2044 Planarity : 0.004 0.049 2204 Dihedral : 5.970 59.057 2404 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.62 % Allowed : 16.30 % Favored : 82.08 % 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: 0.58 (0.21), residues: 1546 helix: 1.60 (0.18), residues: 706 sheet: -0.90 (0.33), residues: 222 loop : -0.47 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 25 TYR 0.023 0.002 TYR A 435 PHE 0.013 0.001 PHE A 469 TRP 0.016 0.002 TRP B 742 HIS 0.004 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00399 (13156) covalent geometry : angle 0.54894 (17900) SS BOND : bond 0.00302 ( 18) SS BOND : angle 1.48929 ( 36) hydrogen bonds : bond 0.05091 ( 648) hydrogen bonds : angle 4.28576 ( 1854) link_BETA1-4 : bond 0.00252 ( 4) link_BETA1-4 : angle 1.16457 ( 12) link_NAG-ASN : bond 0.00178 ( 6) link_NAG-ASN : angle 2.31780 ( 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 210 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.464 Fit side-chains REVERT: A 270 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 516 LYS cc_start: 0.7619 (ttpp) cc_final: 0.7360 (pptt) REVERT: B 257 GLU cc_start: 0.7560 (tp30) cc_final: 0.7135 (tm-30) REVERT: B 265 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8240 (mtpm) REVERT: B 270 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8126 (t80) REVERT: B 475 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: B 818 TRP cc_start: 0.8250 (m100) cc_final: 0.7972 (m100) outliers start: 22 outliers final: 14 residues processed: 198 average time/residue: 0.5867 time to fit residues: 126.3954 Evaluate side-chains 205 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 529 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET 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 475 GLU 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 695 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: 10.0000 chunk 65 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 135 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 359 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 = 0.4157 r_free = 0.4157 target = 0.180065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155967 restraints weight = 17080.447| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.76 r_work: 0.3563 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13184 Z= 0.181 Angle : 0.576 11.300 17966 Z= 0.299 Chirality : 0.043 0.195 2044 Planarity : 0.004 0.046 2204 Dihedral : 5.967 59.559 2404 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.62 % Allowed : 16.45 % Favored : 81.93 % 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: 1.55 (0.18), residues: 706 sheet: -0.93 (0.33), residues: 222 loop : -0.49 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 25 TYR 0.023 0.002 TYR A 435 PHE 0.013 0.001 PHE B 788 TRP 0.017 0.002 TRP B 742 HIS 0.004 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00414 (13156) covalent geometry : angle 0.56809 (17900) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.49820 ( 36) hydrogen bonds : bond 0.05079 ( 648) hydrogen bonds : angle 4.30254 ( 1854) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 1.12834 ( 12) link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 2.32149 ( 18) =============================================================================== Job complete usr+sys time: 4911.48 seconds wall clock time: 84 minutes 10.55 seconds (5050.55 seconds total)