Starting phenix.real_space_refine on Wed Mar 4 10:36:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e6t_30996/03_2026/7e6t_30996.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.098 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 6 9.91 5 P 2 5.49 5 S 74 5.16 5 C 8263 2.51 5 N 2059 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 12741 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6306 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 29, 'TRANS': 763} Chain breaks: 3 Chain: "A" Number of atoms: 6331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6331 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 29, 'TRANS': 766} Chain breaks: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {' CA': 3, 'NAG': 2, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {' CA': 3, 'NAG': 2, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.97, per 1000 atoms: 0.23 Number of scatterers: 12741 At special positions: 0 Unit cell: (103.87, 97.24, 185.64, 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 6 19.99 S 74 16.00 P 2 15.00 O 2337 8.00 N 2059 7.00 C 8263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 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 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 661 " - pdb=" SG CYS B 691 " 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 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 661 " - pdb=" SG CYS A 691 " 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 NAG-ASN " NAG A 905 " - " ASN A 488 " " NAG A 906 " - " ASN A 541 " " NAG B 905 " - " ASN B 488 " " NAG B 906 " - " ASN B 541 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 473.3 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 45.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.956A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.516A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 4.243A pdb=" N GLN B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.723A pdb=" N GLU B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 removed outlier: 3.578A pdb=" N ILE B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) 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 335 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 437 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.697A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.798A pdb=" N GLY B 532 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 632 removed outlier: 3.947A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 removed outlier: 3.630A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.523A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 688 " --> pdb=" O PHE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 708 removed outlier: 4.430A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 728 removed outlier: 3.798A pdb=" N VAL B 728 " --> pdb=" O PHE B 725 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 725 through 728' Processing helix chain 'B' and resid 729 through 746 Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.871A pdb=" N GLY B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 Processing helix chain 'B' and resid 821 through 827 Processing helix chain 'B' and resid 828 through 831 removed outlier: 3.554A pdb=" N LYS B 831 " --> pdb=" O THR B 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 828 through 831' Processing helix chain 'B' and resid 832 through 853 removed outlier: 3.640A pdb=" N PHE B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.515A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.581A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.956A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.721A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.678A pdb=" N ILE A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.529A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.613A pdb=" N GLY A 447 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.649A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) 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 627 Processing helix chain 'A' and resid 627 through 632 removed outlier: 4.095A pdb=" N LEU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 664 removed outlier: 4.030A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 684 through 707 removed outlier: 4.379A pdb=" N PHE A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 removed outlier: 3.965A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.785A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.751A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 827 Processing helix chain 'A' and resid 832 through 853 removed outlier: 3.620A pdb=" N PHE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 859 removed outlier: 4.127A pdb=" N ILE A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 853 through 859' Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.639A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 37 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.833A pdb=" N ASN B 130 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A 130 " --> pdb=" O ASN B 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.080A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 268 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 269 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.239A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AA6, first strand: chain 'B' and resid 550 through 553 Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AA9, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.074A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE A 33 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 141 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY A 35 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.969A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 268 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 318 through 321 removed outlier: 7.342A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 553 Processing sheet with id=AB6, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AB7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.624A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 511 hydrogen bonds defined for protein. 1473 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: 1.99 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4008 1.34 - 1.46: 3303 1.46 - 1.58: 5657 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13056 Sorted by residual: bond pdb=" CD1 TCR A 907 " pdb=" C9 TCR A 907 " ideal model delta sigma weight residual 1.489 1.570 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CD1 TCR B 907 " pdb=" C9 TCR B 907 " ideal model delta sigma weight residual 1.489 1.570 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3 PO4 B 901 " pdb=" P PO4 B 901 " ideal model delta sigma weight residual 1.569 1.495 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 13051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 17578 2.52 - 5.04: 116 5.04 - 7.57: 18 7.57 - 10.09: 3 10.09 - 12.61: 2 Bond angle restraints: 17717 Sorted by residual: angle pdb=" N TCR B 907 " pdb=" C9 TCR B 907 " pdb=" CD1 TCR B 907 " ideal model delta sigma weight residual 107.47 120.08 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N TCR A 907 " pdb=" C9 TCR A 907 " pdb=" CD1 TCR A 907 " ideal model delta sigma weight residual 107.47 120.07 -12.60 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C GLN A 754 " pdb=" N GLU A 755 " pdb=" CA GLU A 755 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" CA SER B 402 " pdb=" C SER B 402 " pdb=" O SER B 402 " ideal model delta sigma weight residual 120.55 117.36 3.19 1.06e+00 8.90e-01 9.06e+00 angle pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" O SER A 403 " ideal model delta sigma weight residual 120.90 117.83 3.07 1.03e+00 9.43e-01 8.86e+00 ... (remaining 17712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 7117 21.24 - 42.49: 520 42.49 - 63.73: 55 63.73 - 84.98: 16 84.98 - 106.22: 14 Dihedral angle restraints: 7722 sinusoidal: 3090 harmonic: 4632 Sorted by residual: 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 -86.00 -143.53 57.53 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -129.81 43.81 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS B 661 " pdb=" SG CYS B 661 " pdb=" SG CYS B 691 " pdb=" CB CYS B 691 " ideal model delta sinusoidal sigma weight residual -86.00 -52.46 -33.54 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 7719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1632 0.051 - 0.103: 292 0.103 - 0.154: 58 0.154 - 0.205: 1 0.205 - 0.257: 1 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA ILE B 401 " pdb=" N ILE B 401 " pdb=" C ILE B 401 " pdb=" CB ILE B 401 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA GLU A 755 " pdb=" N GLU A 755 " pdb=" C GLU A 755 " pdb=" CB GLU A 755 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1981 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 610 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 611 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 610 " -0.027 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 611 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.017 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR A 421 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.002 2.00e-02 2.50e+03 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 31 2.46 - 3.07: 8229 3.07 - 3.68: 18297 3.68 - 4.29: 25710 4.29 - 4.90: 43685 Nonbonded interactions: 95952 Sorted by model distance: nonbonded pdb=" OH TYR A 489 " pdb="CA CA A 902 " model vdw 1.853 2.510 nonbonded pdb=" OE1 GLU A 80 " pdb=" OH TYR A 425 " model vdw 2.191 3.040 nonbonded pdb=" O4 NAG A 905 " pdb=" O7 NAG A 905 " model vdw 2.223 3.040 nonbonded pdb=" O LEU A 87 " pdb=" NE2 GLN A 432 " model vdw 2.248 3.120 nonbonded pdb=" OG SER B 693 " pdb=" OE1 GLN B 735 " model vdw 2.266 3.040 ... (remaining 95947 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 22 through 124 or resid 128 through 907)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.220 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.003 0.081 13071 Z= 0.165 Angle : 0.546 12.610 17751 Z= 0.284 Chirality : 0.041 0.257 1984 Planarity : 0.003 0.050 2240 Dihedral : 14.783 106.222 4691 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.36 % Allowed : 0.22 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1575 helix: 2.01 (0.21), residues: 592 sheet: 0.04 (0.39), residues: 193 loop : -0.52 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 285 TYR 0.028 0.001 TYR A 421 PHE 0.018 0.001 PHE A 815 TRP 0.006 0.001 TRP A 818 HIS 0.003 0.000 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00305 (13056) covalent geometry : angle 0.54529 (17717) SS BOND : bond 0.00131 ( 11) SS BOND : angle 0.68673 ( 22) hydrogen bonds : bond 0.14308 ( 511) hydrogen bonds : angle 5.40320 ( 1473) link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 0.93510 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.344 Fit side-chains REVERT: B 297 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7328 (tp30) REVERT: B 572 GLU cc_start: 0.6812 (pm20) cc_final: 0.6141 (pm20) REVERT: A 446 ASN cc_start: 0.7660 (t0) cc_final: 0.7404 (t0) REVERT: A 811 MET cc_start: 0.6845 (ppp) cc_final: 0.6626 (ppp) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 0.5249 time to fit residues: 59.9666 Evaluate side-chains 68 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 409 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107031 restraints weight = 15490.021| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.56 r_work: 0.2996 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13071 Z= 0.168 Angle : 0.591 8.063 17751 Z= 0.306 Chirality : 0.044 0.154 1984 Planarity : 0.004 0.052 2240 Dihedral : 5.365 56.522 1789 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.94 % Allowed : 7.74 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1575 helix: 1.54 (0.21), residues: 620 sheet: -0.57 (0.36), residues: 198 loop : -0.96 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.020 0.002 TYR B 435 PHE 0.018 0.002 PHE B 42 TRP 0.017 0.002 TRP B 293 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00399 (13056) covalent geometry : angle 0.58666 (17717) SS BOND : bond 0.00205 ( 11) SS BOND : angle 0.78586 ( 22) hydrogen bonds : bond 0.05677 ( 511) hydrogen bonds : angle 4.41895 ( 1473) link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 2.57549 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.621 Fit side-chains REVERT: B 90 ASN cc_start: 0.7300 (m-40) cc_final: 0.6638 (t0) REVERT: B 506 LYS cc_start: 0.8261 (tptm) cc_final: 0.8014 (tppt) REVERT: B 572 GLU cc_start: 0.7886 (pm20) cc_final: 0.6910 (pm20) REVERT: A 56 GLU cc_start: 0.7963 (mp0) cc_final: 0.7728 (mp0) REVERT: A 340 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7256 (ttm170) REVERT: A 446 ASN cc_start: 0.7562 (t0) cc_final: 0.7197 (t0) REVERT: A 811 MET cc_start: 0.6713 (ppp) cc_final: 0.6272 (ppp) outliers start: 13 outliers final: 4 residues processed: 81 average time/residue: 0.4502 time to fit residues: 40.9885 Evaluate side-chains 64 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 580 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 0.0020 chunk 152 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS B 463 HIS A 359 HIS A 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.188504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101975 restraints weight = 15544.773| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.61 r_work: 0.3011 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13071 Z= 0.130 Angle : 0.517 8.641 17751 Z= 0.266 Chirality : 0.042 0.156 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.345 56.445 1786 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.94 % Allowed : 9.11 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1575 helix: 1.64 (0.21), residues: 616 sheet: -0.59 (0.37), residues: 192 loop : -1.04 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.016 0.001 TYR A 421 PHE 0.013 0.001 PHE A 656 TRP 0.010 0.001 TRP B 293 HIS 0.008 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00308 (13056) covalent geometry : angle 0.51386 (17717) SS BOND : bond 0.00162 ( 11) SS BOND : angle 0.62263 ( 22) hydrogen bonds : bond 0.04652 ( 511) hydrogen bonds : angle 4.17419 ( 1473) link_NAG-ASN : bond 0.00227 ( 4) link_NAG-ASN : angle 2.05413 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.459 Fit side-chains REVERT: B 90 ASN cc_start: 0.7561 (m-40) cc_final: 0.6822 (t0) REVERT: B 216 ASP cc_start: 0.8330 (t0) cc_final: 0.8112 (t0) REVERT: B 506 LYS cc_start: 0.8441 (tptm) cc_final: 0.8123 (tppt) REVERT: B 572 GLU cc_start: 0.7794 (pm20) cc_final: 0.6822 (pm20) REVERT: A 340 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7378 (ttm170) REVERT: A 446 ASN cc_start: 0.7759 (t0) cc_final: 0.7357 (t0) REVERT: A 734 MET cc_start: 0.8558 (ppp) cc_final: 0.7306 (tmm) REVERT: A 811 MET cc_start: 0.7112 (ppp) cc_final: 0.6745 (ppp) outliers start: 13 outliers final: 3 residues processed: 73 average time/residue: 0.4615 time to fit residues: 37.8370 Evaluate side-chains 59 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 580 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 207 ASN A 359 HIS A 463 HIS A 735 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.183451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096447 restraints weight = 15415.766| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.61 r_work: 0.3011 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13071 Z= 0.218 Angle : 0.596 6.733 17751 Z= 0.315 Chirality : 0.045 0.181 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.694 52.512 1786 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.66 % Allowed : 9.91 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.20), residues: 1575 helix: 1.36 (0.21), residues: 616 sheet: -0.83 (0.36), residues: 202 loop : -1.31 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.019 0.002 TYR A 421 PHE 0.014 0.002 PHE A 469 TRP 0.014 0.002 TRP B 293 HIS 0.007 0.002 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00542 (13056) covalent geometry : angle 0.59136 (17717) SS BOND : bond 0.00275 ( 11) SS BOND : angle 0.95161 ( 22) hydrogen bonds : bond 0.06479 ( 511) hydrogen bonds : angle 4.37255 ( 1473) link_NAG-ASN : bond 0.00385 ( 4) link_NAG-ASN : angle 2.88965 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.480 Fit side-chains REVERT: B 90 ASN cc_start: 0.7866 (m-40) cc_final: 0.6999 (t0) REVERT: B 216 ASP cc_start: 0.8150 (t0) cc_final: 0.7774 (t0) REVERT: B 572 GLU cc_start: 0.7792 (pm20) cc_final: 0.7128 (pm20) REVERT: A 340 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: A 446 ASN cc_start: 0.7522 (t0) cc_final: 0.6998 (t0) REVERT: A 481 GLU cc_start: 0.8138 (pp20) cc_final: 0.7812 (pp20) REVERT: A 734 MET cc_start: 0.8598 (ppp) cc_final: 0.7432 (tmm) REVERT: A 811 MET cc_start: 0.7009 (ppp) cc_final: 0.6678 (ppp) outliers start: 23 outliers final: 7 residues processed: 78 average time/residue: 0.5155 time to fit residues: 44.6627 Evaluate side-chains 61 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 6 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 113 optimal weight: 0.0970 chunk 138 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS A 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.189679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109530 restraints weight = 15439.925| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.02 r_work: 0.3081 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13071 Z= 0.099 Angle : 0.497 10.380 17751 Z= 0.255 Chirality : 0.041 0.149 1984 Planarity : 0.003 0.055 2240 Dihedral : 4.319 53.668 1786 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.59 % Allowed : 10.77 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1575 helix: 1.58 (0.21), residues: 614 sheet: -0.81 (0.38), residues: 190 loop : -1.15 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.013 0.001 TYR B 435 PHE 0.013 0.001 PHE A 656 TRP 0.010 0.001 TRP A 208 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00222 (13056) covalent geometry : angle 0.49469 (17717) SS BOND : bond 0.00127 ( 11) SS BOND : angle 0.58575 ( 22) hydrogen bonds : bond 0.04054 ( 511) hydrogen bonds : angle 4.02842 ( 1473) link_NAG-ASN : bond 0.00302 ( 4) link_NAG-ASN : angle 2.03420 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.325 Fit side-chains REVERT: B 90 ASN cc_start: 0.7630 (m-40) cc_final: 0.6827 (t0) REVERT: B 216 ASP cc_start: 0.8012 (t0) cc_final: 0.7703 (t0) REVERT: B 405 GLU cc_start: 0.7262 (tt0) cc_final: 0.6982 (tm-30) REVERT: B 409 ILE cc_start: 0.8582 (tp) cc_final: 0.8381 (tt) REVERT: B 572 GLU cc_start: 0.7904 (pm20) cc_final: 0.7298 (pm20) REVERT: A 340 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7411 (ttm170) REVERT: A 446 ASN cc_start: 0.7544 (t0) cc_final: 0.7029 (t0) REVERT: A 481 GLU cc_start: 0.8085 (pp20) cc_final: 0.7801 (pp20) REVERT: A 499 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 734 MET cc_start: 0.8597 (ppp) cc_final: 0.7552 (tmm) REVERT: A 811 MET cc_start: 0.7007 (ppp) cc_final: 0.6678 (ppp) outliers start: 22 outliers final: 6 residues processed: 72 average time/residue: 0.5368 time to fit residues: 42.7095 Evaluate side-chains 61 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 8 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.187749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102132 restraints weight = 15502.607| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.56 r_work: 0.3038 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13071 Z= 0.142 Angle : 0.526 9.433 17751 Z= 0.272 Chirality : 0.042 0.149 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.385 54.989 1786 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.45 % Allowed : 12.00 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1575 helix: 1.55 (0.21), residues: 618 sheet: -0.82 (0.38), residues: 190 loop : -1.20 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.017 0.001 TYR A 421 PHE 0.013 0.001 PHE B 589 TRP 0.011 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00345 (13056) covalent geometry : angle 0.52320 (17717) SS BOND : bond 0.00179 ( 11) SS BOND : angle 0.68997 ( 22) hydrogen bonds : bond 0.04943 ( 511) hydrogen bonds : angle 4.06681 ( 1473) link_NAG-ASN : bond 0.00241 ( 4) link_NAG-ASN : angle 2.22803 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.455 Fit side-chains REVERT: B 90 ASN cc_start: 0.7812 (m-40) cc_final: 0.6942 (t0) REVERT: B 405 GLU cc_start: 0.7400 (tt0) cc_final: 0.6969 (tm-30) REVERT: B 572 GLU cc_start: 0.7907 (pm20) cc_final: 0.7294 (pm20) REVERT: B 589 PHE cc_start: 0.6724 (m-80) cc_final: 0.6134 (m-80) REVERT: A 340 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7408 (ttm170) REVERT: A 446 ASN cc_start: 0.7496 (t0) cc_final: 0.6944 (t0) REVERT: A 499 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 811 MET cc_start: 0.6972 (ppp) cc_final: 0.6697 (ppp) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.5561 time to fit residues: 43.0176 Evaluate side-chains 60 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 463 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 139 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101865 restraints weight = 15426.711| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.54 r_work: 0.3037 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13071 Z= 0.148 Angle : 0.539 8.386 17751 Z= 0.279 Chirality : 0.042 0.149 1984 Planarity : 0.004 0.054 2240 Dihedral : 4.450 55.109 1786 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.66 % Allowed : 12.08 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1575 helix: 1.41 (0.21), residues: 623 sheet: -0.87 (0.38), residues: 190 loop : -1.27 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 54 TYR 0.016 0.001 TYR A 421 PHE 0.012 0.001 PHE A 656 TRP 0.010 0.001 TRP B 293 HIS 0.008 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00361 (13056) covalent geometry : angle 0.53292 (17717) SS BOND : bond 0.00282 ( 11) SS BOND : angle 1.64960 ( 22) hydrogen bonds : bond 0.04968 ( 511) hydrogen bonds : angle 4.08114 ( 1473) link_NAG-ASN : bond 0.00252 ( 4) link_NAG-ASN : angle 2.22704 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.462 Fit side-chains REVERT: B 90 ASN cc_start: 0.7815 (m-40) cc_final: 0.6948 (t0) REVERT: B 572 GLU cc_start: 0.7965 (pm20) cc_final: 0.7303 (pm20) REVERT: B 589 PHE cc_start: 0.6810 (m-80) cc_final: 0.6292 (m-80) REVERT: B 761 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6858 (tp) REVERT: A 340 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: A 446 ASN cc_start: 0.7482 (t0) cc_final: 0.6932 (t0) REVERT: A 499 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7866 (tm-30) REVERT: A 734 MET cc_start: 0.8489 (ppp) cc_final: 0.7243 (tmm) REVERT: A 811 MET cc_start: 0.6985 (ppp) cc_final: 0.6601 (ppp) outliers start: 23 outliers final: 9 residues processed: 72 average time/residue: 0.5270 time to fit residues: 42.2723 Evaluate side-chains 65 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 0.6980 chunk 147 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.190558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105603 restraints weight = 15273.627| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.55 r_work: 0.3116 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13071 Z= 0.095 Angle : 0.501 8.832 17751 Z= 0.253 Chirality : 0.041 0.145 1984 Planarity : 0.003 0.056 2240 Dihedral : 4.256 57.906 1786 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 13.02 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1575 helix: 1.57 (0.21), residues: 618 sheet: -0.80 (0.39), residues: 190 loop : -1.14 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.012 0.001 TYR B 435 PHE 0.012 0.001 PHE A 656 TRP 0.012 0.001 TRP A 208 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00211 (13056) covalent geometry : angle 0.49721 (17717) SS BOND : bond 0.00144 ( 11) SS BOND : angle 1.08490 ( 22) hydrogen bonds : bond 0.03596 ( 511) hydrogen bonds : angle 3.94208 ( 1473) link_NAG-ASN : bond 0.00272 ( 4) link_NAG-ASN : angle 1.85554 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.450 Fit side-chains REVERT: B 90 ASN cc_start: 0.7707 (m-40) cc_final: 0.6884 (t0) REVERT: B 572 GLU cc_start: 0.7878 (pm20) cc_final: 0.7208 (pm20) REVERT: B 589 PHE cc_start: 0.6793 (m-80) cc_final: 0.5968 (m-80) REVERT: B 761 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6841 (tp) REVERT: B 815 PHE cc_start: 0.4791 (OUTLIER) cc_final: 0.4476 (m-80) REVERT: A 340 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7512 (ttm170) REVERT: A 446 ASN cc_start: 0.7524 (t0) cc_final: 0.6968 (t0) REVERT: A 499 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 734 MET cc_start: 0.8495 (ppp) cc_final: 0.7274 (tmm) REVERT: A 811 MET cc_start: 0.6981 (ppp) cc_final: 0.6654 (ppp) outliers start: 15 outliers final: 8 residues processed: 67 average time/residue: 0.5668 time to fit residues: 42.0791 Evaluate side-chains 65 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.188976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103823 restraints weight = 15363.587| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.56 r_work: 0.3049 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13071 Z= 0.118 Angle : 0.516 8.874 17751 Z= 0.262 Chirality : 0.041 0.148 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.290 58.783 1786 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.37 % Allowed : 12.87 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1575 helix: 1.56 (0.21), residues: 618 sheet: -0.81 (0.39), residues: 190 loop : -1.15 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 54 TYR 0.014 0.001 TYR A 421 PHE 0.012 0.001 PHE A 656 TRP 0.009 0.001 TRP B 293 HIS 0.008 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00280 (13056) covalent geometry : angle 0.51297 (17717) SS BOND : bond 0.00167 ( 11) SS BOND : angle 1.05350 ( 22) hydrogen bonds : bond 0.04199 ( 511) hydrogen bonds : angle 3.94686 ( 1473) link_NAG-ASN : bond 0.00219 ( 4) link_NAG-ASN : angle 1.99440 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.483 Fit side-chains REVERT: B 90 ASN cc_start: 0.7772 (m-40) cc_final: 0.6917 (t0) REVERT: B 572 GLU cc_start: 0.7891 (pm20) cc_final: 0.7215 (pm20) REVERT: B 589 PHE cc_start: 0.6758 (m-80) cc_final: 0.6069 (m-80) REVERT: B 761 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6804 (tp) REVERT: A 340 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7404 (ttm170) REVERT: A 446 ASN cc_start: 0.7570 (t0) cc_final: 0.7009 (t0) REVERT: A 499 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 734 MET cc_start: 0.8529 (ppp) cc_final: 0.7352 (tmm) REVERT: A 811 MET cc_start: 0.6959 (ppp) cc_final: 0.6640 (ppp) outliers start: 19 outliers final: 12 residues processed: 66 average time/residue: 0.5475 time to fit residues: 40.0409 Evaluate side-chains 67 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 61 optimal weight: 0.0770 chunk 56 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103086 restraints weight = 15373.378| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.54 r_work: 0.3052 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13071 Z= 0.126 Angle : 0.531 12.794 17751 Z= 0.267 Chirality : 0.042 0.151 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.334 58.434 1786 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.30 % Allowed : 12.94 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1575 helix: 1.55 (0.21), residues: 617 sheet: -0.81 (0.39), residues: 190 loop : -1.16 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 54 TYR 0.015 0.001 TYR A 421 PHE 0.012 0.001 PHE A 656 TRP 0.009 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00302 (13056) covalent geometry : angle 0.52755 (17717) SS BOND : bond 0.00170 ( 11) SS BOND : angle 1.02795 ( 22) hydrogen bonds : bond 0.04445 ( 511) hydrogen bonds : angle 3.96882 ( 1473) link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 2.02959 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.536 Fit side-chains REVERT: B 90 ASN cc_start: 0.7769 (m-40) cc_final: 0.6931 (t0) REVERT: B 572 GLU cc_start: 0.7983 (pm20) cc_final: 0.7320 (pm20) REVERT: B 589 PHE cc_start: 0.6909 (m-80) cc_final: 0.6281 (m-80) REVERT: B 761 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6860 (tp) REVERT: A 340 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: A 446 ASN cc_start: 0.7571 (t0) cc_final: 0.7013 (t0) REVERT: A 499 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 734 MET cc_start: 0.8560 (ppp) cc_final: 0.7445 (tmm) REVERT: A 811 MET cc_start: 0.6967 (ppp) cc_final: 0.6701 (ppp) outliers start: 18 outliers final: 11 residues processed: 68 average time/residue: 0.5296 time to fit residues: 40.1273 Evaluate side-chains 65 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 463 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101961 restraints weight = 15313.100| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.54 r_work: 0.3055 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13071 Z= 0.145 Angle : 0.548 13.276 17751 Z= 0.278 Chirality : 0.042 0.152 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.406 57.632 1786 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.52 % Allowed : 12.94 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1575 helix: 1.52 (0.21), residues: 611 sheet: -0.86 (0.39), residues: 190 loop : -1.17 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 54 TYR 0.016 0.001 TYR A 421 PHE 0.013 0.001 PHE A 469 TRP 0.009 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00354 (13056) covalent geometry : angle 0.54463 (17717) SS BOND : bond 0.00179 ( 11) SS BOND : angle 1.04021 ( 22) hydrogen bonds : bond 0.04853 ( 511) hydrogen bonds : angle 4.01953 ( 1473) link_NAG-ASN : bond 0.00236 ( 4) link_NAG-ASN : angle 2.12833 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.60 seconds wall clock time: 85 minutes 41.47 seconds (5141.47 seconds total)