Starting phenix.real_space_refine on Fri Jul 3 07:48:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e6t_30996/07_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_30996/07_2026/7e6t_30996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e6t_30996/07_2026/7e6t_30996.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 2 Time building chain proxies: 2.49, per 1000 atoms: 0.20 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: 0.87 Conformation dependent library (CDL) restraints added in 585.2 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: 0.31 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: 1.87 Time building geometry restraints manager: 1.26 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 - 17.33: 6854 17.33 - 34.66: 652 34.66 - 52.00: 104 52.00 - 69.33: 24 69.33 - 86.66: 4 Dihedral angle restraints: 7638 sinusoidal: 3006 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 7635 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: 3.060 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.150 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 13.358 86.661 4607 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/Z covalent geometry : bond 0.00305 / 0.16 (13056) covalent geometry : angle 0.54529 / 0.28 (17717) SS BOND : bond 0.00131 / 0.08 ( 11) SS BOND : angle 0.68673 / 0.48 ( 22) hydrogen bonds : bond 0.14308 / 9.46 ( 511) hydrogen bonds : angle 5.40320 / 3.87 ( 1473) link_NAG-ASN : bond 0.00221 / 0.13 ( 4) link_NAG-ASN : angle 0.93510 / 0.54 ( 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 : 0.463 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: 0.6142 (pm20) REVERT: A 446 ASN cc_start: 0.7660 (t0) cc_final: 0.7403 (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: 0.4608 time to fit residues: 52.8196 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 : 0.312 ------------------------------------------------------------------------------- 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... A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.187705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107423 restraints weight = 15469.580| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.43 r_work: 0.2997 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13071 Z= 0.168 Angle : 0.586 7.175 17751 Z= 0.304 Chirality : 0.044 0.188 1984 Planarity : 0.004 0.054 2240 Dihedral : 3.859 38.250 1705 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.94 % Allowed : 7.66 % Favored : 91.40 % 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: 0.18 (0.20), residues: 1575 helix: 1.56 (0.21), residues: 620 sheet: -0.52 (0.36), residues: 200 loop : -0.92 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.020 0.001 TYR B 435 PHE 0.017 0.002 PHE B 42 TRP 0.016 0.002 TRP B 293 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13056) covalent geometry : angle 0.58267 / 0.30 (17717) SS BOND : bond 0.00201 / 0.10 ( 11) SS BOND : angle 0.79622 / 0.47 ( 22) hydrogen bonds : bond 0.05637 / 3.95 ( 511) hydrogen bonds : angle 4.42717 / 3.17 ( 1473) link_NAG-ASN : bond 0.00316 / 0.16 ( 4) link_NAG-ASN : angle 2.49574 / 1.41 ( 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 80 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.338 Fit side-chains REVERT: B 90 ASN cc_start: 0.7339 (m-40) cc_final: 0.6644 (t0) REVERT: B 506 LYS cc_start: 0.8179 (tptm) cc_final: 0.7881 (tppt) REVERT: B 572 GLU cc_start: 0.7779 (pm20) cc_final: 0.6753 (pm20) REVERT: A 56 GLU cc_start: 0.7939 (mp0) cc_final: 0.7683 (mp0) REVERT: A 340 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7238 (ttm170) REVERT: A 446 ASN cc_start: 0.7548 (t0) cc_final: 0.7183 (t0) REVERT: A 734 MET cc_start: 0.8750 (ppp) cc_final: 0.7565 (tmm) REVERT: A 811 MET cc_start: 0.6713 (ppp) cc_final: 0.6246 (ppp) outliers start: 13 outliers final: 4 residues processed: 79 average time/residue: 0.3897 time to fit residues: 34.5797 Evaluate side-chains 65 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 0.0970 chunk 152 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 HIS B 463 HIS A 359 HIS A 466 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 = 0.4206 r_free = 0.4206 target = 0.185856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108004 restraints weight = 15430.121| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.70 r_work: 0.3009 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13071 Z= 0.181 Angle : 0.564 6.985 17751 Z= 0.295 Chirality : 0.044 0.186 1984 Planarity : 0.004 0.055 2240 Dihedral : 4.001 21.202 1702 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.23 % Allowed : 8.97 % Favored : 89.80 % 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: -0.14 (0.20), residues: 1575 helix: 1.43 (0.21), residues: 621 sheet: -0.77 (0.35), residues: 206 loop : -1.22 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.020 0.002 TYR A 421 PHE 0.015 0.001 PHE A 347 TRP 0.012 0.001 TRP A 293 HIS 0.008 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (13056) covalent geometry : angle 0.55985 / 0.29 (17717) SS BOND : bond 0.00233 / 0.11 ( 11) SS BOND : angle 0.82657 / 0.51 ( 22) hydrogen bonds : bond 0.05747 / 3.97 ( 511) hydrogen bonds : angle 4.31049 / 3.06 ( 1473) link_NAG-ASN : bond 0.00293 / 0.15 ( 4) link_NAG-ASN : angle 2.38817 / 1.29 ( 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 82 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.337 Fit side-chains REVERT: B 90 ASN cc_start: 0.7722 (m-40) cc_final: 0.6875 (t0) REVERT: B 216 ASP cc_start: 0.8145 (t0) cc_final: 0.7921 (t0) REVERT: B 572 GLU cc_start: 0.7749 (pm20) cc_final: 0.6835 (pm20) REVERT: A 340 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7397 (ttm170) REVERT: A 446 ASN cc_start: 0.7572 (t0) cc_final: 0.7112 (t0) REVERT: A 580 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8477 (p) REVERT: A 811 MET cc_start: 0.7088 (ppp) cc_final: 0.6752 (ppp) outliers start: 17 outliers final: 5 residues processed: 76 average time/residue: 0.4599 time to fit residues: 39.0276 Evaluate side-chains 62 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR 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: 2.9990 chunk 154 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 359 HIS A 207 ASN A 359 HIS A 463 HIS A 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.188274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102884 restraints weight = 15345.022| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.56 r_work: 0.3040 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3026 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= 0.138 Angle : 0.520 6.598 17751 Z= 0.271 Chirality : 0.042 0.182 1984 Planarity : 0.004 0.055 2240 Dihedral : 3.867 19.587 1702 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 10.12 % 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: -0.07 (0.20), residues: 1575 helix: 1.52 (0.21), residues: 614 sheet: -0.75 (0.37), residues: 194 loop : -1.18 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 25 TYR 0.015 0.001 TYR A 421 PHE 0.013 0.001 PHE A 656 TRP 0.010 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13056) covalent geometry : angle 0.51709 / 0.27 (17717) SS BOND : bond 0.00174 / 0.08 ( 11) SS BOND : angle 0.68294 / 0.41 ( 22) hydrogen bonds : bond 0.04853 / 3.37 ( 511) hydrogen bonds : angle 4.14510 / 2.95 ( 1473) link_NAG-ASN : bond 0.00273 / 0.15 ( 4) link_NAG-ASN : angle 2.19357 / 1.17 ( 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 80 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.360 Fit side-chains REVERT: B 90 ASN cc_start: 0.7807 (m-40) cc_final: 0.6953 (t0) REVERT: B 216 ASP cc_start: 0.8125 (t0) cc_final: 0.7763 (t0) REVERT: B 405 GLU cc_start: 0.7474 (tt0) cc_final: 0.7039 (tm-30) REVERT: B 572 GLU cc_start: 0.7718 (pm20) cc_final: 0.6772 (pm20) REVERT: A 340 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7408 (ttm170) REVERT: A 446 ASN cc_start: 0.7514 (t0) cc_final: 0.6994 (t0) REVERT: A 481 GLU cc_start: 0.8175 (pp20) cc_final: 0.7942 (pp20) REVERT: A 499 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 734 MET cc_start: 0.8539 (ppp) cc_final: 0.7255 (tmm) REVERT: A 811 MET cc_start: 0.6998 (ppp) cc_final: 0.6681 (ppp) outliers start: 20 outliers final: 5 residues processed: 78 average time/residue: 0.4571 time to fit residues: 39.8777 Evaluate side-chains 64 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 A residue 87 LEU 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: 2.9990 chunk 130 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4247 r_free = 0.4247 target = 0.189276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109351 restraints weight = 15444.203| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.99 r_work: 0.3031 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3085 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= 0.112 Angle : 0.499 7.210 17751 Z= 0.255 Chirality : 0.042 0.177 1984 Planarity : 0.003 0.055 2240 Dihedral : 3.727 17.609 1702 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 11.28 % 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 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: -0.00 (0.21), residues: 1575 helix: 1.55 (0.21), residues: 619 sheet: -0.78 (0.38), residues: 190 loop : -1.11 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.014 0.001 TYR A 421 PHE 0.015 0.001 PHE B 589 TRP 0.009 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (13056) covalent geometry : angle 0.49652 / 0.25 (17717) SS BOND : bond 0.00150 / 0.07 ( 11) SS BOND : angle 0.62046 / 0.37 ( 22) hydrogen bonds : bond 0.04262 / 2.96 ( 511) hydrogen bonds : angle 4.00919 / 2.85 ( 1473) link_NAG-ASN : bond 0.00227 / 0.13 ( 4) link_NAG-ASN : angle 1.93249 / 1.05 ( 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 79 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.491 Fit side-chains REVERT: B 90 ASN cc_start: 0.7672 (m-40) cc_final: 0.6833 (t0) REVERT: B 216 ASP cc_start: 0.7991 (t0) cc_final: 0.7782 (t0) REVERT: B 405 GLU cc_start: 0.7276 (tt0) cc_final: 0.6927 (tm-30) REVERT: B 572 GLU cc_start: 0.7780 (pm20) cc_final: 0.7142 (pm20) REVERT: B 589 PHE cc_start: 0.6667 (m-80) cc_final: 0.5782 (m-80) REVERT: A 340 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7379 (ttm170) REVERT: A 446 ASN cc_start: 0.7543 (t0) cc_final: 0.7018 (t0) REVERT: A 499 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 734 MET cc_start: 0.8564 (ppp) cc_final: 0.7368 (tmm) REVERT: A 811 MET cc_start: 0.7005 (ppp) cc_final: 0.6692 (ppp) outliers start: 20 outliers final: 9 residues processed: 74 average time/residue: 0.5269 time to fit residues: 43.4698 Evaluate side-chains 65 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 478 THR Chi-restraints excluded: chain A residue 679 LEU 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: 0.8980 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4208 r_free = 0.4208 target = 0.185059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099675 restraints weight = 15389.721| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.54 r_work: 0.3021 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13071 Z= 0.207 Angle : 0.579 7.766 17751 Z= 0.302 Chirality : 0.045 0.188 1984 Planarity : 0.004 0.054 2240 Dihedral : 4.106 22.932 1702 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.74 % Allowed : 11.79 % 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 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: -0.22 (0.20), residues: 1575 helix: 1.43 (0.21), residues: 611 sheet: -0.87 (0.38), residues: 192 loop : -1.28 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 54 TYR 0.020 0.002 TYR A 421 PHE 0.014 0.001 PHE A 469 TRP 0.014 0.001 TRP B 293 HIS 0.007 0.001 HIS A 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (13056) covalent geometry : angle 0.57470 / 0.30 (17717) SS BOND : bond 0.00254 / 0.12 ( 11) SS BOND : angle 0.90786 / 0.57 ( 22) hydrogen bonds : bond 0.06088 / 4.24 ( 511) hydrogen bonds : angle 4.25099 / 3.01 ( 1473) link_NAG-ASN : bond 0.00265 / 0.14 ( 4) link_NAG-ASN : angle 2.45198 / 1.32 ( 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 79 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.505 Fit side-chains REVERT: B 90 ASN cc_start: 0.7834 (m-40) cc_final: 0.6962 (t0) REVERT: B 216 ASP cc_start: 0.8088 (t0) cc_final: 0.7848 (t0) REVERT: B 572 GLU cc_start: 0.8003 (pm20) cc_final: 0.7335 (pm20) REVERT: B 761 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6791 (tp) REVERT: A 340 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: A 446 ASN cc_start: 0.7525 (t0) cc_final: 0.6966 (t0) REVERT: A 499 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 734 MET cc_start: 0.8564 (ppp) cc_final: 0.7393 (tmm) REVERT: A 811 MET cc_start: 0.6971 (ppp) cc_final: 0.6709 (ppp) outliers start: 24 outliers final: 12 residues processed: 72 average time/residue: 0.4724 time to fit residues: 38.1677 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 : 0.488 ------------------------------------------------------------------------------- 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 761 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4224 r_free = 0.4224 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101695 restraints weight = 15386.232| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.53 r_work: 0.3048 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13071 Z= 0.143 Angle : 0.539 7.709 17751 Z= 0.277 Chirality : 0.043 0.173 1984 Planarity : 0.004 0.056 2240 Dihedral : 3.983 20.226 1702 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.81 % Allowed : 12.29 % 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: -0.20 (0.21), residues: 1575 helix: 1.44 (0.21), residues: 611 sheet: -0.99 (0.37), residues: 204 loop : -1.20 (0.21), residues: 760 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 0.010 0.001 TRP B 293 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (13056) covalent geometry : angle 0.53347 / 0.28 (17717) SS BOND : bond 0.00376 / 0.22 ( 11) SS BOND : angle 1.60638 / 1.12 ( 22) hydrogen bonds : bond 0.04934 / 3.42 ( 511) hydrogen bonds : angle 4.11023 / 2.92 ( 1473) link_NAG-ASN : bond 0.00244 / 0.14 ( 4) link_NAG-ASN : angle 2.15147 / 1.16 ( 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: 25 poor density : 53 time to evaluate : 0.380 Fit side-chains REVERT: B 90 ASN cc_start: 0.7818 (m-40) cc_final: 0.6942 (t0) REVERT: B 216 ASP cc_start: 0.8013 (t0) cc_final: 0.7803 (t0) REVERT: B 572 GLU cc_start: 0.8025 (pm20) cc_final: 0.7349 (pm20) REVERT: B 761 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6732 (tp) REVERT: A 340 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7402 (ttm170) REVERT: A 446 ASN cc_start: 0.7464 (t0) cc_final: 0.6911 (t0) REVERT: A 499 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 734 MET cc_start: 0.8554 (ppp) cc_final: 0.7346 (tmm) REVERT: A 811 MET cc_start: 0.6952 (ppp) cc_final: 0.6588 (ppp) outliers start: 25 outliers final: 11 residues processed: 72 average time/residue: 0.4711 time to fit residues: 37.8869 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 : 0.485 ------------------------------------------------------------------------------- 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 679 LEU Chi-restraints excluded: chain B residue 761 ILE 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 521 LEU 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 116 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 48 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.188267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103432 restraints weight = 15221.551| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.50 r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3506 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= 0.124 Angle : 0.521 9.492 17751 Z= 0.266 Chirality : 0.042 0.170 1984 Planarity : 0.004 0.057 2240 Dihedral : 3.843 18.341 1702 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.52 % Allowed : 13.09 % Favored : 85.39 % 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 (0.21), residues: 1575 helix: 1.50 (0.21), residues: 611 sheet: -0.96 (0.38), residues: 200 loop : -1.16 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 54 TYR 0.015 0.001 TYR A 421 PHE 0.020 0.001 PHE B 656 TRP 0.010 0.001 TRP A 208 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (13056) covalent geometry : angle 0.51740 / 0.26 (17717) SS BOND : bond 0.00241 / 0.13 ( 11) SS BOND : angle 1.19911 / 0.82 ( 22) hydrogen bonds : bond 0.04474 / 3.10 ( 511) hydrogen bonds : angle 4.04500 / 2.88 ( 1473) link_NAG-ASN : bond 0.00225 / 0.13 ( 4) link_NAG-ASN : angle 1.93339 / 1.06 ( 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 74 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.463 Fit side-chains REVERT: B 90 ASN cc_start: 0.7754 (m-40) cc_final: 0.6911 (t0) REVERT: B 572 GLU cc_start: 0.8032 (pm20) cc_final: 0.7334 (pm20) REVERT: B 761 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6730 (tp) REVERT: A 340 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7395 (ttm170) REVERT: A 446 ASN cc_start: 0.7510 (t0) cc_final: 0.6953 (t0) REVERT: A 499 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 734 MET cc_start: 0.8533 (ppp) cc_final: 0.7385 (tmm) REVERT: A 811 MET cc_start: 0.6970 (ppp) cc_final: 0.6659 (ppp) outliers start: 21 outliers final: 12 residues processed: 67 average time/residue: 0.4726 time to fit residues: 35.3136 Evaluate side-chains 66 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 599 ILE 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: 0.5980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 70 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4243 r_free = 0.4243 target = 0.189085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.110777 restraints weight = 15334.396| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.73 r_work: 0.3060 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13071 Z= 0.104 Angle : 0.514 10.831 17751 Z= 0.260 Chirality : 0.041 0.168 1984 Planarity : 0.004 0.057 2240 Dihedral : 3.747 16.776 1702 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.45 % Allowed : 13.23 % Favored : 85.32 % 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: -0.06 (0.21), residues: 1575 helix: 1.55 (0.21), residues: 611 sheet: -0.91 (0.38), residues: 200 loop : -1.13 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 54 TYR 0.013 0.001 TYR A 421 PHE 0.012 0.001 PHE A 656 TRP 0.011 0.001 TRP A 208 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (13056) covalent geometry : angle 0.51068 / 0.26 (17717) SS BOND : bond 0.00158 / 0.08 ( 11) SS BOND : angle 1.03705 / 0.71 ( 22) hydrogen bonds : bond 0.04060 / 2.81 ( 511) hydrogen bonds : angle 3.96888 / 2.83 ( 1473) link_NAG-ASN : bond 0.00239 / 0.15 ( 4) link_NAG-ASN : angle 1.83420 / 1.01 ( 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 73 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.296 Fit side-chains REVERT: B 90 ASN cc_start: 0.7756 (m-40) cc_final: 0.6921 (t0) REVERT: B 572 GLU cc_start: 0.8070 (pm20) cc_final: 0.7355 (pm20) REVERT: B 761 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6828 (tp) REVERT: A 340 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7479 (ttm170) REVERT: A 446 ASN cc_start: 0.7560 (t0) cc_final: 0.7010 (t0) REVERT: A 499 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 734 MET cc_start: 0.8444 (ppp) cc_final: 0.7343 (tmm) outliers start: 20 outliers final: 12 residues processed: 67 average time/residue: 0.5173 time to fit residues: 38.0732 Evaluate side-chains 66 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4234 r_free = 0.4234 target = 0.188261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103469 restraints weight = 15360.731| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.53 r_work: 0.3056 rms_B_bonded: 2.91 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: 0.7871 moved from start: 0.3545 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= 0.124 Angle : 0.526 11.424 17751 Z= 0.267 Chirality : 0.042 0.172 1984 Planarity : 0.004 0.057 2240 Dihedral : 3.775 17.749 1702 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.45 % Allowed : 13.45 % Favored : 85.10 % 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: 611 sheet: -0.92 (0.38), residues: 200 loop : -1.14 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 535 TYR 0.014 0.001 TYR A 421 PHE 0.012 0.001 PHE B 589 TRP 0.009 0.001 TRP B 293 HIS 0.008 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (13056) covalent geometry : angle 0.52256 / 0.27 (17717) SS BOND : bond 0.00174 / 0.09 ( 11) SS BOND : angle 1.03097 / 0.70 ( 22) hydrogen bonds : bond 0.04446 / 3.09 ( 511) hydrogen bonds : angle 3.98639 / 2.84 ( 1473) link_NAG-ASN : bond 0.00203 / 0.12 ( 4) link_NAG-ASN : angle 1.87408 / 1.03 ( 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: 20 poor density : 52 time to evaluate : 0.395 Fit side-chains REVERT: B 90 ASN cc_start: 0.7752 (m-40) cc_final: 0.6894 (t0) REVERT: B 572 GLU cc_start: 0.8007 (pm20) cc_final: 0.7288 (pm20) REVERT: B 761 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6756 (tp) REVERT: B 811 MET cc_start: 0.5953 (tpt) cc_final: 0.5467 (tmm) REVERT: A 340 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: A 446 ASN cc_start: 0.7551 (t0) cc_final: 0.6996 (t0) REVERT: A 499 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 734 MET cc_start: 0.8442 (ppp) cc_final: 0.7343 (tmm) outliers start: 20 outliers final: 12 residues processed: 67 average time/residue: 0.4818 time to fit residues: 35.7505 Evaluate side-chains 66 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain A residue 521 LEU 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: 0.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 82 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4229 r_free = 0.4229 target = 0.187621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102587 restraints weight = 15305.263| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.52 r_work: 0.3060 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3619 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= 0.139 Angle : 0.537 12.290 17751 Z= 0.273 Chirality : 0.042 0.175 1984 Planarity : 0.004 0.057 2240 Dihedral : 3.830 18.710 1702 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.45 % Allowed : 13.74 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1575 helix: 1.52 (0.21), residues: 611 sheet: -0.95 (0.38), residues: 200 loop : -1.17 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 535 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/Z covalent geometry : bond 0.00338 / 0.14 (13056) covalent geometry : angle 0.53403 / 0.27 (17717) SS BOND : bond 0.00181 / 0.08 ( 11) SS BOND : angle 1.03193 / 0.69 ( 22) hydrogen bonds : bond 0.04741 / 3.30 ( 511) hydrogen bonds : angle 4.01360 / 2.86 ( 1473) link_NAG-ASN : bond 0.00213 / 0.12 ( 4) link_NAG-ASN : angle 1.92488 / 1.07 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.26 seconds wall clock time: 69 minutes 50.96 seconds (4190.96 seconds total)