Starting phenix.real_space_refine on Sat Jul 4 06:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.map" model { file = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tvz_26142/07_2026/7tvz_26142.cif" } resolution = 3.6 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= 0.004 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12124 2.51 5 N 3115 2.21 5 O 3348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18659 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6663 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 52, 'TRANS': 797} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6489 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 50, 'TRANS': 774} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5240 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 31, 'TRANS': 633} Chain breaks: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 1, 'LMT': 2, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 147 Unusual residues: {'CLR': 1, 'LMT': 3, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.64, per 1000 atoms: 0.20 Number of scatterers: 18659 At special positions: 0 Unit cell: (111.1, 141.9, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3348 8.00 N 3115 7.00 C 12124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 A1001 " - " ASN A 642 " " NAG B1102 " - " ASN B 642 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4374 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 20 sheets defined 48.3% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.571A pdb=" N HIS A 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 4.236A pdb=" N LYS A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.911A pdb=" N GLU A 168 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 4.053A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.757A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.837A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.896A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.635A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.772A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.694A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 4.016A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.515A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.539A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.511A pdb=" N ALA A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.881A pdb=" N LYS A 695 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 786 through 799 removed outlier: 4.004A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.807A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.574A pdb=" N HIS A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.654A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.779A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.588A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.506A pdb=" N GLU B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.092A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 335 through 347 Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.541A pdb=" N VAL B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.806A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 437 through 455 removed outlier: 3.549A pdb=" N PHE B 451 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.625A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.736A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.659A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.903A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.612A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.651A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.697A pdb=" N ALA B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 720 Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 4.280A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.865A pdb=" N ASP B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.511A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 removed outlier: 3.514A pdb=" N LEU B 835 " --> pdb=" O TRP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 872 removed outlier: 3.873A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 867 " --> pdb=" O LEU B 863 " (cutoff:3.500A) Proline residue: B 868 - end of helix Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'E' and resid 13 through 21 removed outlier: 4.520A pdb=" N GLU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 removed outlier: 3.673A pdb=" N LYS E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.790A pdb=" N ARG E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 201 through 206 removed outlier: 4.117A pdb=" N SER E 206 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 227 removed outlier: 3.736A pdb=" N VAL E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.633A pdb=" N LEU E 242 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 258 Processing helix chain 'E' and resid 269 through 283 removed outlier: 4.388A pdb=" N ALA E 273 " --> pdb=" O TRP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 Processing helix chain 'E' and resid 381 through 388 Processing helix chain 'E' and resid 432 through 435 Processing helix chain 'E' and resid 441 through 458 removed outlier: 3.511A pdb=" N LYS E 445 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.155A pdb=" N ALA A 35 " --> pdb=" O ARG E 638 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.858A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS A 56 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR A 58 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL A 229 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 60 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A 231 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG A 263 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ALA A 226 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 265 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 228 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL A 267 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 230 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU A 269 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG A 263 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 118 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ARG A 246 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 120 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN A 248 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 122 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N ALA A 250 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.858A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.809A pdb=" N LEU A 319 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA6, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.863A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87 removed outlier: 7.080A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 123 removed outlier: 4.486A pdb=" N VAL B 119 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ARG B 246 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU B 121 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 248 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 123 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA B 250 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG B 263 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA B 226 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N PHE B 266 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 228 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 268 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 230 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR B 58 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL B 229 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B 60 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 231 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B 62 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AB2, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.927A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 7 through 12 removed outlier: 3.666A pdb=" N SER E 9 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG E 97 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR E 103 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 93 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER E 91 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 34 removed outlier: 5.653A pdb=" N LEU E 130 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 121 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY E 132 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E 115 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 169 Processing sheet with id=AB6, first strand: chain 'E' and resid 363 through 367 removed outlier: 3.553A pdb=" N ASP E 364 " --> pdb=" O HIS E 350 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR E 330 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N THR E 328 " --> pdb=" O PRO E 351 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE E 323 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA E 295 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE E 325 " --> pdb=" O ALA E 293 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL E 288 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS E 421 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE E 292 " --> pdb=" O ASN E 417 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN E 417 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 308 removed outlier: 5.980A pdb=" N ILE E 304 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TRP E 396 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU E 306 " --> pdb=" O TRP E 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.749A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 408 through 409 removed outlier: 6.749A pdb=" N ASP E 408 " --> pdb=" O PHE E 578 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N GLN E 580 " --> pdb=" O ASP E 408 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA E 515 " --> pdb=" O LYS E 525 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS E 525 " --> pdb=" O ALA E 515 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 475 through 480 Processing sheet with id=AC2, first strand: chain 'E' and resid 590 through 593 904 hydrogen bonds defined for protein. 2577 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: 3.37 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5926 1.34 - 1.46: 4194 1.46 - 1.58: 8837 1.58 - 1.70: 7 1.70 - 1.82: 121 Bond restraints: 19085 Sorted by residual: bond pdb=" C15 CLR A1003 " pdb=" C16 CLR A1003 " ideal model delta sigma weight residual 1.541 1.715 -0.174 2.00e-02 2.50e+03 7.58e+01 bond pdb=" C15 CLR B1104 " pdb=" C16 CLR B1104 " ideal model delta sigma weight residual 1.541 1.714 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C10 CLR A1003 " pdb=" C9 CLR A1003 " ideal model delta sigma weight residual 1.551 1.390 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C10 CLR B1104 " pdb=" C9 CLR B1104 " ideal model delta sigma weight residual 1.551 1.395 0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" C5 CLR A1003 " pdb=" C6 CLR A1003 " ideal model delta sigma weight residual 1.332 1.472 -0.140 2.00e-02 2.50e+03 4.87e+01 ... (remaining 19080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 25378 1.70 - 3.39: 423 3.39 - 5.09: 71 5.09 - 6.78: 48 6.78 - 8.48: 19 Bond angle restraints: 25939 Sorted by residual: angle pdb=" C ARG E 638 " pdb=" N PHE E 639 " pdb=" CA PHE E 639 " ideal model delta sigma weight residual 121.87 127.31 -5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" CB MET E 456 " pdb=" CG MET E 456 " pdb=" SD MET E 456 " ideal model delta sigma weight residual 112.70 121.18 -8.48 3.00e+00 1.11e-01 7.99e+00 angle pdb=" C6 LMT A1004 " pdb=" C7 LMT A1004 " pdb=" C8 LMT A1004 " ideal model delta sigma weight residual 117.26 108.80 8.46 3.00e+00 1.11e-01 7.95e+00 angle pdb=" C1B LMT A1004 " pdb=" O1B LMT A1004 " pdb=" C4' LMT A1004 " ideal model delta sigma weight residual 117.87 110.00 7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" C6 LMT B1103 " pdb=" C7 LMT B1103 " pdb=" C8 LMT B1103 " ideal model delta sigma weight residual 117.26 109.42 7.84 3.00e+00 1.11e-01 6.83e+00 ... (remaining 25934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10214 17.57 - 35.14: 926 35.14 - 52.71: 156 52.71 - 70.28: 25 70.28 - 87.85: 18 Dihedral angle restraints: 11339 sinusoidal: 4581 harmonic: 6758 Sorted by residual: dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PRO A 568 " pdb=" C PRO A 568 " pdb=" N ASN A 569 " pdb=" CA ASN A 569 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLN E 225 " pdb=" C GLN E 225 " pdb=" N ARG E 226 " pdb=" CA ARG E 226 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 11336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2868 0.090 - 0.181: 160 0.181 - 0.271: 2 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 3036 Sorted by residual: chirality pdb=" C9 CLR A1003 " pdb=" C10 CLR A1003 " pdb=" C11 CLR A1003 " pdb=" C8 CLR A1003 " both_signs ideal model delta sigma weight residual False -2.45 -2.90 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C9 CLR B1104 " pdb=" C10 CLR B1104 " pdb=" C11 CLR B1104 " pdb=" C8 CLR B1104 " both_signs ideal model delta sigma weight residual False -2.45 -2.87 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C14 CLR A1003 " pdb=" C13 CLR A1003 " pdb=" C15 CLR A1003 " pdb=" C8 CLR A1003 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3033 not shown) Planarity restraints: 3251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 447 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLN A 447 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN A 447 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY A 448 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 831 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C TRP A 831 " 0.051 2.00e-02 2.50e+03 pdb=" O TRP A 831 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 832 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 638 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ARG E 638 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG E 638 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE E 639 " 0.015 2.00e-02 2.50e+03 ... (remaining 3248 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1509 2.74 - 3.28: 17570 3.28 - 3.82: 28375 3.82 - 4.36: 32181 4.36 - 4.90: 58668 Nonbonded interactions: 138303 Sorted by model distance: nonbonded pdb=" OE1 GLU B 472 " pdb=" OH TYR B 486 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 303 " pdb=" OE1 GLU A 306 " model vdw 2.220 3.040 nonbonded pdb=" O PRO A 271 " pdb=" OH TYR A 278 " model vdw 2.316 3.040 nonbonded pdb=" O2B LMT B1101 " pdb=" O6' LMT B1101 " model vdw 2.316 3.040 nonbonded pdb=" NE2 GLN E 600 " pdb=" O THR E 657 " model vdw 2.318 3.120 ... (remaining 138298 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 55 through 894) selection = (chain 'B' and (resid 55 through 349 or (resid 350 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 through 894)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 19087 Z= 0.238 Angle : 0.611 8.479 25945 Z= 0.270 Chirality : 0.044 0.451 3036 Planarity : 0.004 0.054 3249 Dihedral : 13.963 87.848 6965 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 0.35 (0.17), residues: 2322 helix: 1.62 (0.17), residues: 1009 sheet: 0.35 (0.28), residues: 341 loop : -1.34 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 427 TYR 0.013 0.001 TYR B 519 PHE 0.013 0.001 PHE E 79 TRP 0.016 0.001 TRP B 723 HIS 0.003 0.000 HIS E 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (19085) covalent geometry : angle 0.61121 / 0.27 (25939) hydrogen bonds : bond 0.13921 / 8.95 ( 892) hydrogen bonds : angle 5.32074 / 3.69 ( 2577) link_NAG-ASN : bond 0.00155 / 0.08 ( 2) link_NAG-ASN : angle 0.81205 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9103 (m) cc_final: 0.8693 (p) REVERT: A 72 GLU cc_start: 0.7073 (pp20) cc_final: 0.6597 (pp20) REVERT: A 73 LEU cc_start: 0.8320 (mp) cc_final: 0.7988 (mp) REVERT: A 803 ILE cc_start: 0.7972 (mm) cc_final: 0.7395 (mt) REVERT: E 157 GLU cc_start: 0.8358 (tp30) cc_final: 0.8108 (tp30) REVERT: E 309 ASN cc_start: 0.8053 (t0) cc_final: 0.7833 (t0) REVERT: E 643 TRP cc_start: 0.7985 (m100) cc_final: 0.7779 (m100) REVERT: E 674 GLN cc_start: 0.8665 (mp10) cc_final: 0.8093 (mt0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1477 time to fit residues: 87.1439 Evaluate side-chains 180 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 275 HIS A 521 GLN A 547 HIS A 651 HIS A 683 GLN A 759 GLN B 547 HIS E 64 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127386 restraints weight = 30047.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129826 restraints weight = 52020.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132355 restraints weight = 27020.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133272 restraints weight = 17918.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134471 restraints weight = 15656.782| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19087 Z= 0.239 Angle : 0.696 9.895 25945 Z= 0.340 Chirality : 0.045 0.179 3036 Planarity : 0.005 0.061 3249 Dihedral : 5.740 58.106 2587 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.15 % Allowed : 9.81 % Favored : 88.04 % 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: 0.23 (0.17), residues: 2322 helix: 1.44 (0.17), residues: 1012 sheet: 0.22 (0.28), residues: 346 loop : -1.30 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 97 TYR 0.027 0.002 TYR A 824 PHE 0.024 0.002 PHE E 134 TRP 0.020 0.002 TRP E 333 HIS 0.007 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (19085) covalent geometry : angle 0.69627 / 0.34 (25939) hydrogen bonds : bond 0.05944 / 3.99 ( 892) hydrogen bonds : angle 4.66724 / 3.22 ( 2577) link_NAG-ASN : bond 0.00638 / 0.31 ( 2) link_NAG-ASN : angle 0.87625 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7697 (ttp) cc_final: 0.7436 (ttt) REVERT: A 641 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8371 (m) REVERT: A 803 ILE cc_start: 0.8235 (mm) cc_final: 0.7602 (mt) REVERT: B 66 MET cc_start: 0.6588 (ptt) cc_final: 0.6289 (ptp) REVERT: E 81 ILE cc_start: 0.8816 (mp) cc_final: 0.8536 (mt) REVERT: E 157 GLU cc_start: 0.8556 (tp30) cc_final: 0.8269 (tp30) REVERT: E 308 TYR cc_start: 0.8532 (m-80) cc_final: 0.8283 (m-10) REVERT: E 674 GLN cc_start: 0.8870 (mp10) cc_final: 0.8298 (mt0) outliers start: 43 outliers final: 21 residues processed: 219 average time/residue: 0.1413 time to fit residues: 47.4325 Evaluate side-chains 179 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 641 SER Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 147 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN B 593 ASN ** E 570 HIS ** 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 = 0.3976 r_free = 0.3976 target = 0.162850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124742 restraints weight = 30200.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123058 restraints weight = 35222.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119043 restraints weight = 22780.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119459 restraints weight = 23633.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120146 restraints weight = 20013.406| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19087 Z= 0.142 Angle : 0.574 9.493 25945 Z= 0.278 Chirality : 0.041 0.201 3036 Planarity : 0.005 0.060 3249 Dihedral : 5.510 57.743 2587 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.00 % Allowed : 11.56 % Favored : 86.44 % 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: 0.45 (0.17), residues: 2322 helix: 1.62 (0.17), residues: 1015 sheet: 0.36 (0.28), residues: 351 loop : -1.19 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.022 0.002 TYR A 824 PHE 0.017 0.001 PHE A 471 TRP 0.017 0.001 TRP A 662 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (19085) covalent geometry : angle 0.57365 / 0.28 (25939) hydrogen bonds : bond 0.04889 / 3.31 ( 892) hydrogen bonds : angle 4.36565 / 3.01 ( 2577) link_NAG-ASN : bond 0.00265 / 0.13 ( 2) link_NAG-ASN : angle 0.93759 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7688 (ttp) cc_final: 0.7365 (ttt) REVERT: A 759 GLN cc_start: 0.7658 (mp10) cc_final: 0.7266 (mp10) REVERT: A 803 ILE cc_start: 0.8295 (mm) cc_final: 0.7672 (mt) REVERT: A 887 ASP cc_start: 0.7169 (t0) cc_final: 0.6847 (m-30) REVERT: B 435 MET cc_start: 0.7758 (mtp) cc_final: 0.7349 (mtt) REVERT: B 864 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7506 (tp) REVERT: E 308 TYR cc_start: 0.8494 (m-80) cc_final: 0.8151 (m-10) REVERT: E 674 GLN cc_start: 0.8919 (mp10) cc_final: 0.8204 (mt0) outliers start: 40 outliers final: 29 residues processed: 204 average time/residue: 0.1225 time to fit residues: 39.6878 Evaluate side-chains 187 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 116 optimal weight: 0.9990 chunk 159 optimal weight: 0.0670 chunk 66 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 218 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN E 76 GLN ** E 570 HIS ** 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 = 0.3995 r_free = 0.3995 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126059 restraints weight = 30025.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125705 restraints weight = 34615.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121797 restraints weight = 20970.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121656 restraints weight = 22189.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122678 restraints weight = 19609.819| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19087 Z= 0.108 Angle : 0.531 9.253 25945 Z= 0.254 Chirality : 0.039 0.160 3036 Planarity : 0.004 0.062 3249 Dihedral : 5.171 58.544 2587 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.95 % Allowed : 13.41 % Favored : 84.63 % 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: 0.66 (0.17), residues: 2322 helix: 1.80 (0.17), residues: 1019 sheet: 0.33 (0.28), residues: 355 loop : -1.05 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 16 TYR 0.020 0.001 TYR A 824 PHE 0.013 0.001 PHE B 511 TRP 0.012 0.001 TRP A 831 HIS 0.006 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (19085) covalent geometry : angle 0.53047 / 0.25 (25939) hydrogen bonds : bond 0.04051 / 2.75 ( 892) hydrogen bonds : angle 4.15022 / 2.87 ( 2577) link_NAG-ASN : bond 0.00266 / 0.13 ( 2) link_NAG-ASN : angle 0.94939 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 433 ASN cc_start: 0.7554 (t0) cc_final: 0.7295 (t0) REVERT: A 803 ILE cc_start: 0.7976 (mm) cc_final: 0.7263 (mt) REVERT: A 887 ASP cc_start: 0.7114 (t0) cc_final: 0.6907 (m-30) REVERT: B 186 GLN cc_start: 0.6051 (mm-40) cc_final: 0.5417 (tp40) REVERT: B 281 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8016 (tt) REVERT: B 496 TRP cc_start: 0.7235 (m100) cc_final: 0.6803 (m100) REVERT: E 308 TYR cc_start: 0.8435 (m-80) cc_final: 0.8160 (m-10) REVERT: E 309 ASN cc_start: 0.7886 (m-40) cc_final: 0.7626 (m-40) REVERT: E 674 GLN cc_start: 0.8860 (mp10) cc_final: 0.8156 (mt0) outliers start: 39 outliers final: 21 residues processed: 204 average time/residue: 0.1178 time to fit residues: 38.6192 Evaluate side-chains 182 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 211 optimal weight: 5.9990 chunk 124 optimal weight: 0.0070 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 22 optimal weight: 0.0010 chunk 65 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 457 GLN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.166113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131282 restraints weight = 29856.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134608 restraints weight = 49235.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136547 restraints weight = 25408.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137333 restraints weight = 17460.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.138541 restraints weight = 15572.578| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19087 Z= 0.094 Angle : 0.517 13.792 25945 Z= 0.245 Chirality : 0.039 0.158 3036 Planarity : 0.004 0.062 3249 Dihedral : 4.874 53.926 2587 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 14.86 % Favored : 83.28 % 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: 0.81 (0.18), residues: 2322 helix: 1.89 (0.17), residues: 1028 sheet: 0.44 (0.28), residues: 353 loop : -0.97 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 782 TYR 0.018 0.001 TYR A 824 PHE 0.020 0.001 PHE B 511 TRP 0.008 0.001 TRP A 662 HIS 0.005 0.000 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (19085) covalent geometry : angle 0.51703 / 0.24 (25939) hydrogen bonds : bond 0.03550 / 2.42 ( 892) hydrogen bonds : angle 4.01184 / 2.79 ( 2577) link_NAG-ASN : bond 0.00261 / 0.13 ( 2) link_NAG-ASN : angle 0.88741 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7822 (mp10) cc_final: 0.7240 (mp10) REVERT: A 803 ILE cc_start: 0.8040 (mm) cc_final: 0.7326 (mt) REVERT: B 142 GLU cc_start: 0.8312 (tp30) cc_final: 0.8019 (tm-30) REVERT: B 186 GLN cc_start: 0.5771 (mm-40) cc_final: 0.5425 (tp40) REVERT: B 496 TRP cc_start: 0.7196 (m100) cc_final: 0.6829 (m100) REVERT: B 864 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7605 (tp) REVERT: E 308 TYR cc_start: 0.8428 (m-80) cc_final: 0.8200 (m-10) REVERT: E 674 GLN cc_start: 0.8773 (mp10) cc_final: 0.8176 (mt0) outliers start: 37 outliers final: 22 residues processed: 207 average time/residue: 0.1341 time to fit residues: 44.3871 Evaluate side-chains 186 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126678 restraints weight = 29983.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130879 restraints weight = 52264.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132617 restraints weight = 22408.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133287 restraints weight = 16786.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134249 restraints weight = 14262.208| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19087 Z= 0.167 Angle : 0.583 10.824 25945 Z= 0.280 Chirality : 0.041 0.161 3036 Planarity : 0.005 0.059 3249 Dihedral : 5.002 55.314 2587 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.40 % Allowed : 15.37 % Favored : 82.23 % 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: 0.66 (0.18), residues: 2322 helix: 1.75 (0.17), residues: 1027 sheet: 0.34 (0.28), residues: 353 loop : -1.01 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.018 0.002 TYR A 824 PHE 0.016 0.002 PHE A 114 TRP 0.014 0.001 TRP B 492 HIS 0.005 0.001 HIS E 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (19085) covalent geometry : angle 0.58312 / 0.28 (25939) hydrogen bonds : bond 0.04743 / 3.22 ( 892) hydrogen bonds : angle 4.22348 / 2.93 ( 2577) link_NAG-ASN : bond 0.00224 / 0.11 ( 2) link_NAG-ASN : angle 0.76307 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: B 186 GLN cc_start: 0.5914 (mm-40) cc_final: 0.5469 (tp40) REVERT: B 496 TRP cc_start: 0.7152 (m100) cc_final: 0.6739 (m100) REVERT: B 864 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7696 (tp) REVERT: E 308 TYR cc_start: 0.8636 (m-80) cc_final: 0.8420 (m-10) REVERT: E 549 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: E 674 GLN cc_start: 0.8849 (mp10) cc_final: 0.8176 (mt0) outliers start: 48 outliers final: 32 residues processed: 203 average time/residue: 0.1304 time to fit residues: 42.9316 Evaluate side-chains 189 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 32 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 189 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124165 restraints weight = 29978.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125448 restraints weight = 36955.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126002 restraints weight = 24472.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125355 restraints weight = 18958.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125799 restraints weight = 18875.061| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19087 Z= 0.117 Angle : 0.552 10.786 25945 Z= 0.263 Chirality : 0.039 0.158 3036 Planarity : 0.004 0.060 3249 Dihedral : 4.896 54.287 2587 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.70 % Allowed : 16.42 % Favored : 81.88 % 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: 0.72 (0.18), residues: 2322 helix: 1.82 (0.17), residues: 1027 sheet: 0.36 (0.27), residues: 353 loop : -1.00 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.017 0.001 TYR A 824 PHE 0.020 0.001 PHE B 659 TRP 0.016 0.001 TRP B 492 HIS 0.006 0.001 HIS E 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19085) covalent geometry : angle 0.55149 / 0.26 (25939) hydrogen bonds : bond 0.04113 / 2.80 ( 892) hydrogen bonds : angle 4.09008 / 2.83 ( 2577) link_NAG-ASN : bond 0.00222 / 0.11 ( 2) link_NAG-ASN : angle 0.78353 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 GLN cc_start: 0.5733 (mm-40) cc_final: 0.5358 (tp40) REVERT: B 496 TRP cc_start: 0.7090 (m100) cc_final: 0.6692 (m100) REVERT: B 864 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7638 (tp) REVERT: E 456 MET cc_start: 0.7990 (mmm) cc_final: 0.7770 (mmm) REVERT: E 674 GLN cc_start: 0.8868 (mp10) cc_final: 0.8225 (mt0) outliers start: 34 outliers final: 23 residues processed: 189 average time/residue: 0.1298 time to fit residues: 39.6844 Evaluate side-chains 178 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 116 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN B 163 HIS E 532 HIS ** E 570 HIS ** 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 = 0.3965 r_free = 0.3965 target = 0.161701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126894 restraints weight = 29803.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129496 restraints weight = 51302.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131592 restraints weight = 25551.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132706 restraints weight = 17387.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133624 restraints weight = 15090.667| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19087 Z= 0.146 Angle : 0.571 10.204 25945 Z= 0.275 Chirality : 0.040 0.166 3036 Planarity : 0.004 0.058 3249 Dihedral : 4.927 56.134 2587 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 16.57 % Favored : 81.28 % 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: 0.63 (0.18), residues: 2322 helix: 1.76 (0.17), residues: 1026 sheet: 0.26 (0.27), residues: 353 loop : -1.04 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.018 0.001 TYR A 824 PHE 0.016 0.001 PHE B 511 TRP 0.013 0.001 TRP B 492 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (19085) covalent geometry : angle 0.57132 / 0.27 (25939) hydrogen bonds : bond 0.04472 / 3.05 ( 892) hydrogen bonds : angle 4.15535 / 2.88 ( 2577) link_NAG-ASN : bond 0.00196 / 0.10 ( 2) link_NAG-ASN : angle 0.74920 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: B 496 TRP cc_start: 0.7106 (m100) cc_final: 0.6618 (m100) REVERT: B 864 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7717 (tp) REVERT: E 456 MET cc_start: 0.8092 (mmm) cc_final: 0.7866 (mmm) REVERT: E 549 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: E 674 GLN cc_start: 0.8867 (mp10) cc_final: 0.8659 (mp10) outliers start: 43 outliers final: 28 residues processed: 197 average time/residue: 0.1279 time to fit residues: 39.9570 Evaluate side-chains 182 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 168 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 171 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.0670 chunk 139 optimal weight: 0.8980 chunk 218 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125324 restraints weight = 29798.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123706 restraints weight = 34200.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120839 restraints weight = 19799.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121166 restraints weight = 22681.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121787 restraints weight = 19001.451| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19087 Z= 0.116 Angle : 0.552 10.237 25945 Z= 0.264 Chirality : 0.040 0.157 3036 Planarity : 0.004 0.059 3249 Dihedral : 4.772 54.293 2587 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.55 % Allowed : 17.32 % Favored : 81.13 % 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: 0.70 (0.18), residues: 2322 helix: 1.80 (0.17), residues: 1028 sheet: 0.31 (0.28), residues: 343 loop : -0.99 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.018 0.001 TYR A 824 PHE 0.017 0.001 PHE B 511 TRP 0.009 0.001 TRP B 75 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19085) covalent geometry : angle 0.55237 / 0.26 (25939) hydrogen bonds : bond 0.04049 / 2.76 ( 892) hydrogen bonds : angle 4.06762 / 2.81 ( 2577) link_NAG-ASN : bond 0.00202 / 0.10 ( 2) link_NAG-ASN : angle 0.78649 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 759 GLN cc_start: 0.7727 (mp10) cc_final: 0.6962 (mp10) REVERT: B 496 TRP cc_start: 0.7102 (m100) cc_final: 0.6563 (m100) REVERT: B 864 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7519 (tp) REVERT: E 456 MET cc_start: 0.8101 (mmm) cc_final: 0.7873 (mmm) REVERT: E 549 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: E 648 MET cc_start: 0.7675 (tmm) cc_final: 0.7079 (tmm) REVERT: E 674 GLN cc_start: 0.8972 (mp10) cc_final: 0.8698 (mp10) outliers start: 31 outliers final: 28 residues processed: 181 average time/residue: 0.1348 time to fit residues: 38.7204 Evaluate side-chains 183 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 128 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 171 optimal weight: 0.0370 chunk 195 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 GLN ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.159918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122672 restraints weight = 29866.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121004 restraints weight = 35597.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117762 restraints weight = 20829.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117994 restraints weight = 21699.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118374 restraints weight = 20300.490| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19087 Z= 0.179 Angle : 0.608 10.148 25945 Z= 0.293 Chirality : 0.042 0.170 3036 Planarity : 0.005 0.058 3249 Dihedral : 4.987 55.628 2587 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 17.22 % Favored : 80.83 % 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: 0.48 (0.17), residues: 2322 helix: 1.64 (0.17), residues: 1026 sheet: 0.18 (0.28), residues: 343 loop : -1.11 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.019 0.002 TYR A 824 PHE 0.018 0.002 PHE B 511 TRP 0.013 0.001 TRP E 333 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (19085) covalent geometry : angle 0.60823 / 0.29 (25939) hydrogen bonds : bond 0.04996 / 3.39 ( 892) hydrogen bonds : angle 4.27898 / 2.96 ( 2577) link_NAG-ASN : bond 0.00167 / 0.08 ( 2) link_NAG-ASN : angle 0.93223 / 0.58 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 675 PHE cc_start: 0.7644 (t80) cc_final: 0.7397 (t80) REVERT: A 759 GLN cc_start: 0.7716 (mp10) cc_final: 0.7000 (mp10) REVERT: B 496 TRP cc_start: 0.7047 (m100) cc_final: 0.6641 (m100) REVERT: B 864 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7560 (tp) REVERT: E 549 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: E 648 MET cc_start: 0.7706 (tmm) cc_final: 0.7112 (tmm) REVERT: E 674 GLN cc_start: 0.9003 (mp10) cc_final: 0.8689 (mp10) outliers start: 39 outliers final: 30 residues processed: 180 average time/residue: 0.1366 time to fit residues: 39.1493 Evaluate side-chains 180 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 67 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123475 restraints weight = 29918.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124250 restraints weight = 34699.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121322 restraints weight = 20103.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120481 restraints weight = 20812.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120890 restraints weight = 19234.258| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19087 Z= 0.113 Angle : 0.560 10.928 25945 Z= 0.266 Chirality : 0.040 0.189 3036 Planarity : 0.004 0.061 3249 Dihedral : 4.775 52.921 2587 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.60 % Allowed : 17.72 % Favored : 80.68 % 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: 0.64 (0.18), residues: 2322 helix: 1.80 (0.17), residues: 1026 sheet: 0.21 (0.28), residues: 343 loop : -1.02 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.019 0.001 TYR A 824 PHE 0.022 0.001 PHE A 294 TRP 0.010 0.001 TRP B 75 HIS 0.003 0.001 HIS A 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (19085) covalent geometry : angle 0.56021 / 0.27 (25939) hydrogen bonds : bond 0.04104 / 2.79 ( 892) hydrogen bonds : angle 4.07820 / 2.82 ( 2577) link_NAG-ASN : bond 0.00221 / 0.11 ( 2) link_NAG-ASN : angle 0.80568 / 0.54 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3002.68 seconds wall clock time: 52 minutes 51.94 seconds (3171.94 seconds total)