Starting phenix.real_space_refine on Thu Jul 31 01:14:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_30996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_30996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_30996.map" model { file = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_30996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2025/7e6t_30996.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.24, per 1000 atoms: 0.65 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: 2.78 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.41 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: 3.96 Time building geometry restraints manager: 3.33 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 861 or resid 901 throu \ gh 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: 1.920 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.500 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (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 TRP 0.006 0.001 TRP A 818 HIS 0.003 0.000 HIS A 463 PHE 0.018 0.001 PHE A 815 TYR 0.028 0.001 TYR A 421 ARG 0.002 0.000 ARG B 285 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 0.93510 ( 12) hydrogen bonds : bond 0.14308 ( 511) hydrogen bonds : angle 5.40320 ( 1473) SS BOND : bond 0.00131 ( 11) SS BOND : angle 0.68673 ( 22) covalent geometry : bond 0.00305 (13056) covalent geometry : angle 0.54529 (17717) *********************** 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 : 1.486 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: 1.1334 time to fit residues: 130.5562 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 : 1.348 ------------------------------------------------------------------------------- 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 133 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.190589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118255 restraints weight = 15403.227| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.38 r_work: 0.3106 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13071 Z= 0.139 Angle : 0.552 7.953 17751 Z= 0.283 Chirality : 0.042 0.167 1984 Planarity : 0.004 0.052 2240 Dihedral : 5.158 57.699 1789 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.94 % Allowed : 7.09 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1575 helix: 1.73 (0.21), residues: 614 sheet: -0.43 (0.37), residues: 200 loop : -0.78 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 293 HIS 0.005 0.001 HIS A 463 PHE 0.014 0.001 PHE B 469 TYR 0.019 0.001 TYR B 435 ARG 0.003 0.000 ARG A 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 4) link_NAG-ASN : angle 2.15973 ( 12) hydrogen bonds : bond 0.04807 ( 511) hydrogen bonds : angle 4.28492 ( 1473) SS BOND : bond 0.00168 ( 11) SS BOND : angle 0.68535 ( 22) covalent geometry : bond 0.00314 (13056) covalent geometry : angle 0.54941 (17717) *********************** 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 81 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.362 Fit side-chains REVERT: B 90 ASN cc_start: 0.7319 (m-40) cc_final: 0.6653 (t0) REVERT: B 297 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8044 (tp30) REVERT: B 572 GLU cc_start: 0.7713 (pm20) cc_final: 0.6852 (pm20) REVERT: A 56 GLU cc_start: 0.7952 (mp0) cc_final: 0.7650 (mp0) REVERT: A 207 ASN cc_start: 0.8415 (m110) cc_final: 0.7970 (m110) REVERT: A 340 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7283 (ttm170) REVERT: A 446 ASN cc_start: 0.7676 (t0) cc_final: 0.7333 (t0) REVERT: A 734 MET cc_start: 0.8725 (ppp) cc_final: 0.7556 (tmm) REVERT: A 811 MET cc_start: 0.6733 (ppp) cc_final: 0.6266 (ppp) outliers start: 13 outliers final: 5 residues processed: 80 average time/residue: 1.0174 time to fit residues: 91.8173 Evaluate side-chains 67 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 401 ILE 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 117 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 0.0040 chunk 118 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 HIS A 359 HIS A 463 HIS A 466 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108902 restraints weight = 15447.965| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.40 r_work: 0.3026 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13071 Z= 0.119 Angle : 0.502 6.817 17751 Z= 0.258 Chirality : 0.041 0.170 1984 Planarity : 0.003 0.055 2240 Dihedral : 4.346 59.934 1786 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.01 % Allowed : 9.33 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1575 helix: 1.76 (0.21), residues: 611 sheet: -0.42 (0.37), residues: 192 loop : -0.93 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.007 0.001 HIS B 463 PHE 0.013 0.001 PHE A 656 TYR 0.016 0.001 TYR A 421 ARG 0.002 0.000 ARG A 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 4) link_NAG-ASN : angle 1.98773 ( 12) hydrogen bonds : bond 0.04387 ( 511) hydrogen bonds : angle 4.12094 ( 1473) SS BOND : bond 0.00165 ( 11) SS BOND : angle 0.58063 ( 22) covalent geometry : bond 0.00277 (13056) covalent geometry : angle 0.49906 (17717) *********************** 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 79 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.261 Fit side-chains REVERT: B 29 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8119 (pmtt) REVERT: B 90 ASN cc_start: 0.7548 (m-40) cc_final: 0.6801 (t0) REVERT: B 216 ASP cc_start: 0.8338 (t0) cc_final: 0.8085 (t0) REVERT: B 217 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 572 GLU cc_start: 0.7618 (pm20) cc_final: 0.6693 (pm20) REVERT: A 56 GLU cc_start: 0.7980 (mp0) cc_final: 0.7681 (mp0) REVERT: A 340 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: A 446 ASN cc_start: 0.7604 (t0) cc_final: 0.7221 (t0) REVERT: A 811 MET cc_start: 0.7117 (ppp) cc_final: 0.6766 (ppp) outliers start: 14 outliers final: 3 residues processed: 77 average time/residue: 0.9104 time to fit residues: 79.6123 Evaluate side-chains 62 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 217 ASP Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain A residue 340 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 73 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.187238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109617 restraints weight = 15202.185| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.71 r_work: 0.3006 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13071 Z= 0.166 Angle : 0.549 6.769 17751 Z= 0.288 Chirality : 0.043 0.152 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.440 54.403 1786 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.59 % Allowed : 10.05 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1575 helix: 1.46 (0.21), residues: 629 sheet: -0.69 (0.37), residues: 196 loop : -1.19 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 PHE 0.013 0.001 PHE A 469 TYR 0.017 0.002 TYR A 421 ARG 0.004 0.000 ARG A 25 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 2.58273 ( 12) hydrogen bonds : bond 0.05602 ( 511) hydrogen bonds : angle 4.21780 ( 1473) SS BOND : bond 0.00210 ( 11) SS BOND : angle 0.77988 ( 22) covalent geometry : bond 0.00408 (13056) covalent geometry : angle 0.54456 (17717) *********************** 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 84 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 1.278 Fit side-chains REVERT: B 29 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8031 (pmtt) REVERT: B 90 ASN cc_start: 0.7657 (m-40) cc_final: 0.6842 (t0) REVERT: B 216 ASP cc_start: 0.7990 (t0) cc_final: 0.7641 (t0) REVERT: B 516 LYS cc_start: 0.7321 (mttp) cc_final: 0.6774 (mtpp) REVERT: B 572 GLU cc_start: 0.7674 (pm20) cc_final: 0.7155 (pm20) REVERT: A 123 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7405 (tt) REVERT: A 340 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7380 (ttm170) REVERT: A 446 ASN cc_start: 0.7519 (t0) cc_final: 0.7019 (t0) REVERT: A 580 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8466 (p) REVERT: A 734 MET cc_start: 0.8532 (ppp) cc_final: 0.7323 (tmm) REVERT: A 811 MET cc_start: 0.7024 (ppp) cc_final: 0.6703 (ppp) outliers start: 22 outliers final: 9 residues processed: 79 average time/residue: 0.9941 time to fit residues: 88.6077 Evaluate side-chains 68 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 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 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 580 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 471 ASN A 673 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.187308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110453 restraints weight = 15356.152| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.80 r_work: 0.3000 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13071 Z= 0.165 Angle : 0.541 9.784 17751 Z= 0.281 Chirality : 0.043 0.161 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.459 53.950 1786 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.66 % Allowed : 11.06 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1575 helix: 1.45 (0.21), residues: 619 sheet: -0.82 (0.37), residues: 194 loop : -1.18 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 293 HIS 0.016 0.002 HIS A 463 PHE 0.013 0.001 PHE A 656 TYR 0.017 0.001 TYR A 421 ARG 0.003 0.000 ARG B 172 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 2.29909 ( 12) hydrogen bonds : bond 0.05305 ( 511) hydrogen bonds : angle 4.15097 ( 1473) SS BOND : bond 0.00200 ( 11) SS BOND : angle 0.75712 ( 22) covalent geometry : bond 0.00404 (13056) covalent geometry : angle 0.53785 (17717) *********************** 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 78 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 1.234 Fit side-chains REVERT: B 90 ASN cc_start: 0.7714 (m-40) cc_final: 0.6862 (t0) REVERT: B 216 ASP cc_start: 0.7978 (t0) cc_final: 0.7763 (t0) REVERT: B 405 GLU cc_start: 0.7332 (tt0) cc_final: 0.6968 (tm-30) REVERT: B 516 LYS cc_start: 0.7405 (mttp) cc_final: 0.6882 (mtpp) REVERT: B 572 GLU cc_start: 0.7862 (pm20) cc_final: 0.7256 (pm20) REVERT: A 123 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7466 (tt) REVERT: A 340 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7384 (ttm170) REVERT: A 446 ASN cc_start: 0.7482 (t0) cc_final: 0.6951 (t0) REVERT: A 481 GLU cc_start: 0.8132 (pp20) cc_final: 0.7820 (pp20) REVERT: A 734 MET cc_start: 0.8517 (ppp) cc_final: 0.7320 (tmm) REVERT: A 811 MET cc_start: 0.6974 (ppp) cc_final: 0.6666 (ppp) outliers start: 23 outliers final: 11 residues processed: 73 average time/residue: 1.0356 time to fit residues: 85.0967 Evaluate side-chains 66 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 271 SER Chi-restraints excluded: chain B residue 409 ILE 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 123 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 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 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102411 restraints weight = 15513.600| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.54 r_work: 0.3042 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13071 Z= 0.140 Angle : 0.519 9.199 17751 Z= 0.268 Chirality : 0.042 0.146 1984 Planarity : 0.004 0.054 2240 Dihedral : 4.381 54.696 1786 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 11.50 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1575 helix: 1.53 (0.21), residues: 612 sheet: -0.88 (0.37), residues: 194 loop : -1.17 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 PHE 0.013 0.001 PHE A 656 TYR 0.016 0.001 TYR A 421 ARG 0.007 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 4) link_NAG-ASN : angle 2.19094 ( 12) hydrogen bonds : bond 0.04779 ( 511) hydrogen bonds : angle 4.07089 ( 1473) SS BOND : bond 0.00190 ( 11) SS BOND : angle 0.70198 ( 22) covalent geometry : bond 0.00341 (13056) covalent geometry : angle 0.51618 (17717) *********************** 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 85 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 1.276 Fit side-chains REVERT: B 90 ASN cc_start: 0.7798 (m-40) cc_final: 0.6953 (t0) REVERT: B 216 ASP cc_start: 0.8000 (t0) cc_final: 0.7799 (t0) REVERT: B 516 LYS cc_start: 0.7433 (mttp) cc_final: 0.6930 (mtpp) REVERT: B 572 GLU cc_start: 0.7941 (pm20) cc_final: 0.7349 (pm20) REVERT: B 589 PHE cc_start: 0.6867 (m-80) cc_final: 0.6332 (m-80) REVERT: A 123 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7533 (tt) REVERT: A 340 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7459 (ttm170) REVERT: A 446 ASN cc_start: 0.7497 (t0) cc_final: 0.6966 (t0) REVERT: A 481 GLU cc_start: 0.8207 (pp20) cc_final: 0.7941 (pp20) REVERT: A 499 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 734 MET cc_start: 0.8543 (ppp) cc_final: 0.7375 (tmm) REVERT: A 811 MET cc_start: 0.6977 (ppp) cc_final: 0.6612 (ppp) outliers start: 28 outliers final: 14 residues processed: 80 average time/residue: 1.0618 time to fit residues: 95.4495 Evaluate side-chains 70 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 86 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 117 optimal weight: 0.0000 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.189644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104539 restraints weight = 15382.295| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.57 r_work: 0.3063 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3278 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= 0.102 Angle : 0.497 8.181 17751 Z= 0.253 Chirality : 0.041 0.145 1984 Planarity : 0.003 0.056 2240 Dihedral : 4.274 56.954 1786 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.37 % Allowed : 12.22 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1575 helix: 1.62 (0.21), residues: 617 sheet: -0.83 (0.38), residues: 190 loop : -1.07 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.007 0.001 HIS B 359 PHE 0.012 0.001 PHE A 656 TYR 0.012 0.001 TYR A 421 ARG 0.009 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.93454 ( 12) hydrogen bonds : bond 0.03940 ( 511) hydrogen bonds : angle 3.93776 ( 1473) SS BOND : bond 0.00225 ( 11) SS BOND : angle 1.25587 ( 22) covalent geometry : bond 0.00231 (13056) covalent geometry : angle 0.49259 (17717) *********************** 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 77 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.361 Fit side-chains REVERT: B 90 ASN cc_start: 0.7722 (m-40) cc_final: 0.6879 (t0) REVERT: B 572 GLU cc_start: 0.7857 (pm20) cc_final: 0.7230 (pm20) REVERT: B 589 PHE cc_start: 0.6832 (m-80) cc_final: 0.6056 (m-80) REVERT: B 761 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6806 (tp) REVERT: A 123 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7505 (tt) REVERT: A 340 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7398 (ttm170) REVERT: A 446 ASN cc_start: 0.7475 (t0) cc_final: 0.6933 (t0) REVERT: A 499 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7810 (tm-30) REVERT: A 734 MET cc_start: 0.8467 (ppp) cc_final: 0.7371 (tmm) REVERT: A 811 MET cc_start: 0.6979 (ppp) cc_final: 0.6677 (ppp) outliers start: 19 outliers final: 10 residues processed: 72 average time/residue: 1.0641 time to fit residues: 86.1857 Evaluate side-chains 66 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 ILE 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 123 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.186815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102013 restraints weight = 15422.059| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.86 r_work: 0.3031 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13071 Z= 0.157 Angle : 0.543 8.411 17751 Z= 0.281 Chirality : 0.043 0.152 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.447 56.642 1786 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.52 % Allowed : 12.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1575 helix: 1.51 (0.21), residues: 611 sheet: -0.87 (0.38), residues: 194 loop : -1.17 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 293 HIS 0.006 0.001 HIS B 359 PHE 0.012 0.001 PHE A 469 TYR 0.017 0.001 TYR A 421 ARG 0.007 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 4) link_NAG-ASN : angle 2.24868 ( 12) hydrogen bonds : bond 0.05203 ( 511) hydrogen bonds : angle 4.10315 ( 1473) SS BOND : bond 0.00236 ( 11) SS BOND : angle 1.28126 ( 22) covalent geometry : bond 0.00386 (13056) covalent geometry : angle 0.53798 (17717) *********************** 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 76 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.272 Fit side-chains REVERT: B 90 ASN cc_start: 0.7818 (m-40) cc_final: 0.6960 (t0) REVERT: B 516 LYS cc_start: 0.7313 (mttp) cc_final: 0.6745 (mtpp) REVERT: B 572 GLU cc_start: 0.8035 (pm20) cc_final: 0.7428 (pm20) REVERT: B 589 PHE cc_start: 0.6941 (m-80) cc_final: 0.6416 (m-80) REVERT: B 761 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6797 (tp) REVERT: A 123 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7500 (tt) REVERT: A 340 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: A 446 ASN cc_start: 0.7530 (t0) cc_final: 0.6970 (t0) REVERT: A 499 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 734 MET cc_start: 0.8447 (ppp) cc_final: 0.7341 (tmm) outliers start: 21 outliers final: 12 residues processed: 70 average time/residue: 1.1141 time to fit residues: 87.4453 Evaluate side-chains 68 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 394 LEU Chi-restraints excluded: chain B residue 454 LYS 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 123 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL 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 148 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104101 restraints weight = 15371.849| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.55 r_work: 0.3095 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3437 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= 0.108 Angle : 0.503 9.028 17751 Z= 0.257 Chirality : 0.041 0.145 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.294 57.018 1786 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 13.09 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1575 helix: 1.58 (0.21), residues: 617 sheet: -0.85 (0.39), residues: 190 loop : -1.10 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.006 0.001 HIS B 359 PHE 0.012 0.001 PHE A 656 TYR 0.013 0.001 TYR A 421 ARG 0.009 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 1.94352 ( 12) hydrogen bonds : bond 0.04031 ( 511) hydrogen bonds : angle 3.97041 ( 1473) SS BOND : bond 0.00146 ( 11) SS BOND : angle 1.01651 ( 22) covalent geometry : bond 0.00250 (13056) covalent geometry : angle 0.49935 (17717) *********************** 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 74 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.375 Fit side-chains REVERT: B 90 ASN cc_start: 0.7708 (m-40) cc_final: 0.6886 (t0) REVERT: B 516 LYS cc_start: 0.7294 (mttp) cc_final: 0.6731 (mtpp) REVERT: B 572 GLU cc_start: 0.7964 (pm20) cc_final: 0.7363 (pm20) REVERT: B 589 PHE cc_start: 0.6788 (m-80) cc_final: 0.6199 (m-80) REVERT: B 761 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6803 (tp) REVERT: A 123 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 340 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7452 (ttm170) REVERT: A 446 ASN cc_start: 0.7561 (t0) cc_final: 0.7009 (t0) REVERT: A 499 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 734 MET cc_start: 0.8440 (ppp) cc_final: 0.7341 (tmm) outliers start: 20 outliers final: 11 residues processed: 67 average time/residue: 1.0851 time to fit residues: 81.7714 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 : 1.267 ------------------------------------------------------------------------------- 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 123 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL 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 90 optimal weight: 2.9990 chunk 148 optimal weight: 0.0030 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 0.0670 chunk 142 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.3528 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.191418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107291 restraints weight = 15458.359| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.55 r_work: 0.3113 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13071 Z= 0.090 Angle : 0.482 9.347 17751 Z= 0.245 Chirality : 0.041 0.143 1984 Planarity : 0.004 0.057 2240 Dihedral : 4.154 59.130 1786 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.08 % Allowed : 13.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1575 helix: 1.72 (0.21), residues: 612 sheet: -0.84 (0.39), residues: 186 loop : -1.03 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.008 0.001 HIS B 359 PHE 0.013 0.001 PHE A 656 TYR 0.011 0.001 TYR B 435 ARG 0.009 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 4) link_NAG-ASN : angle 1.74197 ( 12) hydrogen bonds : bond 0.03367 ( 511) hydrogen bonds : angle 3.85008 ( 1473) SS BOND : bond 0.00122 ( 11) SS BOND : angle 0.89847 ( 22) covalent geometry : bond 0.00199 (13056) covalent geometry : angle 0.47977 (17717) ********************** 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 70 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 1.294 Fit side-chains REVERT: B 90 ASN cc_start: 0.7684 (m-40) cc_final: 0.6865 (t0) REVERT: B 572 GLU cc_start: 0.7846 (pm20) cc_final: 0.7309 (pm20) REVERT: B 589 PHE cc_start: 0.6740 (m-80) cc_final: 0.5935 (m-80) REVERT: B 761 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6807 (tp) REVERT: A 123 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7506 (tt) REVERT: A 340 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7519 (ttm170) REVERT: A 446 ASN cc_start: 0.7571 (t0) cc_final: 0.7023 (t0) REVERT: A 499 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 734 MET cc_start: 0.8453 (ppp) cc_final: 0.7335 (tmm) outliers start: 15 outliers final: 8 residues processed: 64 average time/residue: 1.0151 time to fit residues: 74.6235 Evaluate side-chains 64 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 811 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.187673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102465 restraints weight = 15372.946| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.54 r_work: 0.3044 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13071 Z= 0.142 Angle : 0.526 9.242 17751 Z= 0.271 Chirality : 0.042 0.151 1984 Planarity : 0.004 0.056 2240 Dihedral : 4.352 58.554 1786 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.16 % Allowed : 13.59 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1575 helix: 1.61 (0.21), residues: 612 sheet: -0.87 (0.39), residues: 186 loop : -1.09 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 293 HIS 0.008 0.001 HIS A 463 PHE 0.012 0.001 PHE A 656 TYR 0.016 0.001 TYR A 421 ARG 0.010 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 4) link_NAG-ASN : angle 2.13251 ( 12) hydrogen bonds : bond 0.04811 ( 511) hydrogen bonds : angle 3.99518 ( 1473) SS BOND : bond 0.00176 ( 11) SS BOND : angle 0.98811 ( 22) covalent geometry : bond 0.00346 (13056) covalent geometry : angle 0.52247 (17717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10005.77 seconds wall clock time: 173 minutes 43.26 seconds (10423.26 seconds total)