Starting phenix.real_space_refine on Thu Mar 5 03:57:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tvz_26142/03_2026/7tvz_26142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvz_26142/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tvz_26142/03_2026/7tvz_26142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvz_26142/03_2026/7tvz_26142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tvz_26142/03_2026/7tvz_26142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvz_26142/03_2026/7tvz_26142.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 3 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 dihedrals: 3 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: 4.71, per 1000 atoms: 0.25 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: 1.59 Conformation dependent library (CDL) restraints added in 938.9 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: 0.92 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: 3.62 Time building geometry restraints manager: 2.15 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 - 24.18: 11014 24.18 - 48.37: 632 48.37 - 72.55: 69 72.55 - 96.73: 16 96.73 - 120.92: 12 Dihedral angle restraints: 11743 sinusoidal: 4985 harmonic: 6758 Sorted by residual: dihedral pdb=" C2B LMT B1105 " pdb=" C1B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" C5B LMT B1105 " ideal model delta sinusoidal sigma weight residual -57.12 63.80 -120.92 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C1B LMT B1105 " pdb=" C5B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" C6B LMT B1105 " ideal model delta sinusoidal sigma weight residual 175.31 -63.95 -120.74 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C5B LMT B1105 " pdb=" C1B LMT B1105 " pdb=" O5B LMT B1105 " pdb=" O1B LMT B1105 " ideal model delta sinusoidal sigma weight residual 295.61 176.91 118.70 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 11740 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 14.937 120.916 7369 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 covalent geometry : bond 0.00485 (19085) covalent geometry : angle 0.61121 (25939) hydrogen bonds : bond 0.13921 ( 892) hydrogen bonds : angle 5.32074 ( 2577) link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 0.81205 ( 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 : 0.735 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: 0.1491 time to fit residues: 88.0020 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 : 0.726 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 275 HIS A 521 GLN A 547 HIS A 651 HIS A 683 GLN A 752 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.163003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127688 restraints weight = 29998.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130519 restraints weight = 52517.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133277 restraints weight = 25793.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133804 restraints weight = 17267.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135594 restraints weight = 15176.845| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19087 Z= 0.240 Angle : 0.693 9.691 25945 Z= 0.338 Chirality : 0.045 0.213 3036 Planarity : 0.005 0.063 3249 Dihedral : 8.837 96.659 2991 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 9.66 % Favored : 88.14 % 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: 0.25 (0.17), residues: 2322 helix: 1.48 (0.17), residues: 1012 sheet: 0.19 (0.28), residues: 348 loop : -1.28 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 97 TYR 0.026 0.002 TYR A 824 PHE 0.023 0.002 PHE E 134 TRP 0.020 0.002 TRP E 333 HIS 0.008 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00580 (19085) covalent geometry : angle 0.69342 (25939) hydrogen bonds : bond 0.05916 ( 892) hydrogen bonds : angle 4.65828 ( 2577) link_NAG-ASN : bond 0.00429 ( 2) link_NAG-ASN : angle 0.85612 ( 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: 44 poor density : 189 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7680 (ttp) cc_final: 0.7416 (ttt) REVERT: A 641 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8361 (m) REVERT: A 752 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: A 803 ILE cc_start: 0.8220 (mm) cc_final: 0.7582 (mt) REVERT: B 66 MET cc_start: 0.6531 (ptt) cc_final: 0.6217 (ptp) REVERT: E 81 ILE cc_start: 0.8816 (mp) cc_final: 0.8504 (mt) REVERT: E 157 GLU cc_start: 0.8548 (tp30) cc_final: 0.8249 (tp30) REVERT: E 308 TYR cc_start: 0.8532 (m-80) cc_final: 0.8224 (m-10) REVERT: E 674 GLN cc_start: 0.8896 (mp10) cc_final: 0.8327 (mt0) outliers start: 44 outliers final: 22 residues processed: 221 average time/residue: 0.1458 time to fit residues: 49.5583 Evaluate side-chains 183 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 752 GLN 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 A residue 822 VAL 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: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.160531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121015 restraints weight = 30263.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122686 restraints weight = 37803.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122474 restraints weight = 23274.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121843 restraints weight = 19021.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122285 restraints weight = 18637.462| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19087 Z= 0.202 Angle : 0.631 9.275 25945 Z= 0.307 Chirality : 0.043 0.212 3036 Planarity : 0.005 0.061 3249 Dihedral : 7.508 72.070 2991 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.45 % Allowed : 11.96 % Favored : 85.59 % 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: 0.29 (0.17), residues: 2322 helix: 1.51 (0.17), residues: 1011 sheet: 0.19 (0.28), residues: 343 loop : -1.25 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.023 0.002 TYR A 824 PHE 0.019 0.002 PHE A 836 TRP 0.021 0.002 TRP A 662 HIS 0.005 0.001 HIS E 632 Details of bonding type rmsd covalent geometry : bond 0.00483 (19085) covalent geometry : angle 0.63069 (25939) hydrogen bonds : bond 0.05510 ( 892) hydrogen bonds : angle 4.49730 ( 2577) link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 1.13564 ( 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 223 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7683 (ttp) cc_final: 0.7381 (ttt) REVERT: A 803 ILE cc_start: 0.8250 (mm) cc_final: 0.7623 (mt) REVERT: B 721 MET cc_start: 0.7702 (mpp) cc_final: 0.7049 (mpp) REVERT: B 864 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7714 (tp) REVERT: E 81 ILE cc_start: 0.8847 (mp) cc_final: 0.8549 (mt) REVERT: E 308 TYR cc_start: 0.8594 (m-80) cc_final: 0.8197 (m-10) REVERT: E 674 GLN cc_start: 0.8930 (mp10) cc_final: 0.8169 (mt0) outliers start: 49 outliers final: 31 residues processed: 211 average time/residue: 0.1323 time to fit residues: 44.0168 Evaluate side-chains 190 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 546 ASP 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 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 439 GLU Chi-restraints excluded: chain B residue 470 VAL 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 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 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 560 THR Chi-restraints excluded: chain E residue 641 SER 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: 0.9980 chunk 159 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 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 = 0.3962 r_free = 0.3962 target = 0.161481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126581 restraints weight = 30157.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129546 restraints weight = 53025.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131925 restraints weight = 25549.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132614 restraints weight = 17684.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133408 restraints weight = 15365.295| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2872 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= 0.146 Angle : 0.576 9.381 25945 Z= 0.278 Chirality : 0.041 0.178 3036 Planarity : 0.005 0.063 3249 Dihedral : 6.760 58.837 2991 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.65 % Allowed : 13.41 % Favored : 83.93 % 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: 0.42 (0.17), residues: 2322 helix: 1.64 (0.17), residues: 1016 sheet: 0.15 (0.28), residues: 355 loop : -1.19 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.021 0.002 TYR A 824 PHE 0.015 0.001 PHE B 511 TRP 0.013 0.001 TRP B 492 HIS 0.006 0.001 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00344 (19085) covalent geometry : angle 0.57558 (25939) hydrogen bonds : bond 0.04805 ( 892) hydrogen bonds : angle 4.35132 ( 2577) link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 1.06253 ( 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 219 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 94 TRP cc_start: 0.7645 (m100) cc_final: 0.7378 (m100) REVERT: A 803 ILE cc_start: 0.8287 (mm) cc_final: 0.7663 (mt) REVERT: B 864 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7800 (tp) REVERT: E 81 ILE cc_start: 0.8877 (mp) cc_final: 0.8588 (mt) REVERT: E 308 TYR cc_start: 0.8597 (m-80) cc_final: 0.8327 (m-10) REVERT: E 309 ASN cc_start: 0.7729 (m-40) cc_final: 0.7483 (m-40) REVERT: E 674 GLN cc_start: 0.8889 (mp10) cc_final: 0.8241 (mt0) outliers start: 53 outliers final: 34 residues processed: 209 average time/residue: 0.1196 time to fit residues: 40.4044 Evaluate side-chains 192 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 460 LEU 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 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 140 ILE Chi-restraints excluded: chain B residue 197 THR 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 439 GLU 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 867 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 277 THR Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 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 639 PHE Chi-restraints excluded: chain E residue 665 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: 3.9990 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 171 optimal weight: 0.0470 chunk 166 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 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 = 0.3959 r_free = 0.3959 target = 0.161168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125851 restraints weight = 29937.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128806 restraints weight = 49991.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130746 restraints weight = 24920.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131537 restraints weight = 17357.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133028 restraints weight = 15170.007| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19087 Z= 0.148 Angle : 0.569 9.913 25945 Z= 0.274 Chirality : 0.041 0.174 3036 Planarity : 0.005 0.064 3249 Dihedral : 6.480 57.355 2991 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.70 % Allowed : 15.82 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2322 helix: 1.62 (0.17), residues: 1030 sheet: 0.19 (0.28), residues: 345 loop : -1.15 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.020 0.002 TYR A 824 PHE 0.019 0.001 PHE B 511 TRP 0.015 0.001 TRP B 492 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00355 (19085) covalent geometry : angle 0.56908 (25939) hydrogen bonds : bond 0.04730 ( 892) hydrogen bonds : angle 4.29019 ( 2577) link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 1.00815 ( 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 225 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 433 ASN cc_start: 0.7522 (t0) cc_final: 0.7301 (t0) REVERT: A 759 GLN cc_start: 0.7713 (mp10) cc_final: 0.7019 (mp10) REVERT: B 142 GLU cc_start: 0.8565 (tp30) cc_final: 0.8246 (tm-30) REVERT: B 186 GLN cc_start: 0.6071 (mm-40) cc_final: 0.5769 (tp40) REVERT: B 496 TRP cc_start: 0.7007 (m100) cc_final: 0.6650 (m100) REVERT: B 864 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7819 (tp) REVERT: E 81 ILE cc_start: 0.8904 (mp) cc_final: 0.8635 (mt) REVERT: E 308 TYR cc_start: 0.8658 (m-80) cc_final: 0.8412 (m-10) REVERT: E 309 ASN cc_start: 0.7833 (m-40) cc_final: 0.7620 (m-40) REVERT: E 549 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: E 674 GLN cc_start: 0.8920 (mp10) cc_final: 0.8268 (mt0) outliers start: 54 outliers final: 39 residues processed: 214 average time/residue: 0.1166 time to fit residues: 40.3129 Evaluate side-chains 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET 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 A residue 847 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 197 THR 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 439 GLU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 620 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 867 VAL Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU 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 330 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 200 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS ** 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 = 0.3968 r_free = 0.3968 target = 0.161841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123345 restraints weight = 29937.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125304 restraints weight = 36842.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.125320 restraints weight = 23455.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124655 restraints weight = 19303.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125087 restraints weight = 18351.513| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3192 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= 0.128 Angle : 0.554 10.347 25945 Z= 0.267 Chirality : 0.040 0.173 3036 Planarity : 0.004 0.066 3249 Dihedral : 6.313 59.527 2991 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.75 % Allowed : 16.37 % Favored : 80.88 % 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: 0.55 (0.18), residues: 2322 helix: 1.72 (0.17), residues: 1028 sheet: 0.22 (0.28), residues: 345 loop : -1.11 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 514 TYR 0.017 0.001 TYR A 824 PHE 0.018 0.001 PHE A 294 TRP 0.012 0.001 TRP B 492 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00300 (19085) covalent geometry : angle 0.55375 (25939) hydrogen bonds : bond 0.04380 ( 892) hydrogen bonds : angle 4.19522 ( 2577) link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 0.93123 ( 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 225 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (tt) REVERT: A 433 ASN cc_start: 0.7613 (t0) cc_final: 0.7335 (t0) REVERT: B 186 GLN cc_start: 0.6123 (mm-40) cc_final: 0.5453 (tp40) REVERT: B 496 TRP cc_start: 0.6968 (m100) cc_final: 0.6620 (m100) REVERT: B 719 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: B 864 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7722 (tp) REVERT: E 81 ILE cc_start: 0.8889 (mp) cc_final: 0.8605 (mt) REVERT: E 308 TYR cc_start: 0.8616 (m-80) cc_final: 0.8384 (m-10) REVERT: E 549 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: E 674 GLN cc_start: 0.8945 (mp10) cc_final: 0.8660 (mp10) outliers start: 55 outliers final: 36 residues processed: 213 average time/residue: 0.1248 time to fit residues: 42.9266 Evaluate side-chains 198 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET 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 A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 197 THR 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 350 SER Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 719 PHE Chi-restraints excluded: chain B residue 780 LEU 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 365 LEU 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 549 PHE Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 665 THR 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: 3.9990 chunk 10 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 32 optimal weight: 40.0000 chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 457 GLN A 521 GLN B 163 HIS ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122524 restraints weight = 30016.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.124437 restraints weight = 38162.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124489 restraints weight = 22709.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123582 restraints weight = 19971.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124101 restraints weight = 19424.078| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19087 Z= 0.147 Angle : 0.572 9.221 25945 Z= 0.276 Chirality : 0.041 0.172 3036 Planarity : 0.005 0.064 3249 Dihedral : 6.237 56.804 2991 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.00 % Allowed : 16.72 % Favored : 80.28 % 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: 0.49 (0.18), residues: 2322 helix: 1.68 (0.17), residues: 1028 sheet: 0.16 (0.28), residues: 345 loop : -1.14 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 514 TYR 0.016 0.001 TYR A 824 PHE 0.019 0.001 PHE B 659 TRP 0.018 0.001 TRP B 492 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00351 (19085) covalent geometry : angle 0.57211 (25939) hydrogen bonds : bond 0.04600 ( 892) hydrogen bonds : angle 4.21926 ( 2577) link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 0.94637 ( 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 224 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 433 ASN cc_start: 0.7631 (t0) cc_final: 0.7374 (t0) REVERT: B 186 GLN cc_start: 0.6136 (mm-40) cc_final: 0.5671 (tp40) REVERT: B 496 TRP cc_start: 0.6936 (m100) cc_final: 0.6547 (m100) REVERT: B 719 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: B 864 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7696 (tp) REVERT: E 81 ILE cc_start: 0.8911 (mp) cc_final: 0.8641 (mt) REVERT: E 549 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: E 648 MET cc_start: 0.7719 (tmm) cc_final: 0.7346 (tmm) REVERT: E 674 GLN cc_start: 0.8964 (mp10) cc_final: 0.8671 (mp10) outliers start: 60 outliers final: 43 residues processed: 211 average time/residue: 0.1281 time to fit residues: 43.2135 Evaluate side-chains 204 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 496 TRP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET 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 A residue 864 ILE Chi-restraints excluded: chain A residue 867 VAL 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 197 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 719 PHE Chi-restraints excluded: chain B residue 780 LEU 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 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 330 THR Chi-restraints excluded: chain E residue 365 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 116 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 204 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.162629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124239 restraints weight = 29771.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125407 restraints weight = 36497.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125491 restraints weight = 23961.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125131 restraints weight = 18356.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125537 restraints weight = 18376.685| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19087 Z= 0.112 Angle : 0.551 12.093 25945 Z= 0.263 Chirality : 0.040 0.171 3036 Planarity : 0.004 0.065 3249 Dihedral : 6.052 59.325 2991 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.35 % Allowed : 17.22 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2322 helix: 1.78 (0.17), residues: 1029 sheet: 0.19 (0.28), residues: 345 loop : -1.07 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 80 TYR 0.018 0.001 TYR A 824 PHE 0.019 0.001 PHE B 511 TRP 0.010 0.001 TRP A 81 HIS 0.004 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00257 (19085) covalent geometry : angle 0.55112 (25939) hydrogen bonds : bond 0.03988 ( 892) hydrogen bonds : angle 4.09309 ( 2577) link_NAG-ASN : bond 0.00248 ( 2) link_NAG-ASN : angle 0.87783 ( 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 218 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 433 ASN cc_start: 0.7560 (t0) cc_final: 0.7359 (t0) REVERT: B 186 GLN cc_start: 0.5911 (mm-40) cc_final: 0.5453 (tp40) REVERT: B 496 TRP cc_start: 0.7113 (m100) cc_final: 0.6641 (m100) REVERT: B 664 MET cc_start: 0.7489 (mmm) cc_final: 0.7192 (tpp) REVERT: B 719 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: E 81 ILE cc_start: 0.8869 (mp) cc_final: 0.8602 (mt) REVERT: E 549 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: E 648 MET cc_start: 0.7520 (tmm) cc_final: 0.7051 (tmm) REVERT: E 674 GLN cc_start: 0.8962 (mp10) cc_final: 0.8686 (mp10) outliers start: 47 outliers final: 32 residues processed: 205 average time/residue: 0.1135 time to fit residues: 37.5820 Evaluate side-chains 197 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET 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 864 ILE 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 217 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 719 PHE Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET 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 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 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 677 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 168 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 171 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129584 restraints weight = 29789.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132726 restraints weight = 50636.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133942 restraints weight = 26986.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135993 restraints weight = 18054.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136545 restraints weight = 14659.650| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3462 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= 0.098 Angle : 0.539 11.484 25945 Z= 0.256 Chirality : 0.039 0.165 3036 Planarity : 0.004 0.060 3249 Dihedral : 5.771 57.800 2991 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.60 % Allowed : 18.12 % Favored : 80.28 % 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: 0.74 (0.18), residues: 2322 helix: 1.87 (0.17), residues: 1032 sheet: 0.23 (0.28), residues: 345 loop : -0.97 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 389 TYR 0.017 0.001 TYR A 824 PHE 0.020 0.001 PHE A 294 TRP 0.010 0.001 TRP A 81 HIS 0.004 0.000 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00219 (19085) covalent geometry : angle 0.53895 (25939) hydrogen bonds : bond 0.03621 ( 892) hydrogen bonds : angle 4.00155 ( 2577) link_NAG-ASN : bond 0.00256 ( 2) link_NAG-ASN : angle 0.80285 ( 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 207 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.7560 (t0) cc_final: 0.7353 (t0) REVERT: B 186 GLN cc_start: 0.5886 (mm-40) cc_final: 0.5485 (tp40) REVERT: B 496 TRP cc_start: 0.7097 (m100) cc_final: 0.6613 (m100) REVERT: B 664 MET cc_start: 0.7553 (mmm) cc_final: 0.7309 (tpp) REVERT: B 741 MET cc_start: 0.6682 (tmm) cc_final: 0.5977 (tpp) REVERT: E 81 ILE cc_start: 0.8868 (mp) cc_final: 0.8594 (mt) REVERT: E 549 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.6666 (m-80) outliers start: 32 outliers final: 27 residues processed: 199 average time/residue: 0.1165 time to fit residues: 37.7783 Evaluate side-chains 187 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 712 MET 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 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 831 TRP 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 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 277 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 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 128 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 169 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125724 restraints weight = 29881.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130419 restraints weight = 50504.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131477 restraints weight = 21342.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132154 restraints weight = 16832.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133176 restraints weight = 14207.978| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19087 Z= 0.166 Angle : 0.603 11.420 25945 Z= 0.287 Chirality : 0.041 0.171 3036 Planarity : 0.005 0.061 3249 Dihedral : 5.914 56.031 2991 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.70 % Allowed : 18.22 % Favored : 80.08 % 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: 0.58 (0.18), residues: 2322 helix: 1.74 (0.17), residues: 1028 sheet: 0.15 (0.28), residues: 345 loop : -1.05 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 283 TYR 0.017 0.001 TYR A 824 PHE 0.029 0.002 PHE A 294 TRP 0.013 0.001 TRP B 492 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00403 (19085) covalent geometry : angle 0.60332 (25939) hydrogen bonds : bond 0.04747 ( 892) hydrogen bonds : angle 4.19126 ( 2577) link_NAG-ASN : bond 0.00188 ( 2) link_NAG-ASN : angle 0.90571 ( 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 193 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7458 (mtm110) REVERT: B 186 GLN cc_start: 0.6078 (mm-40) cc_final: 0.5595 (tp40) REVERT: B 496 TRP cc_start: 0.6966 (m100) cc_final: 0.6621 (m100) REVERT: B 664 MET cc_start: 0.7578 (mmm) cc_final: 0.7333 (tpp) REVERT: B 741 MET cc_start: 0.6695 (tmm) cc_final: 0.5957 (tpp) REVERT: E 81 ILE cc_start: 0.8888 (mp) cc_final: 0.8618 (mt) REVERT: E 549 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6756 (m-80) REVERT: E 648 MET cc_start: 0.7657 (tmm) cc_final: 0.7009 (tmm) outliers start: 34 outliers final: 29 residues processed: 187 average time/residue: 0.1316 time to fit residues: 39.1743 Evaluate side-chains 184 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU 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 A residue 847 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 831 TRP 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 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 277 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 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 67 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 229 optimal weight: 0.6980 chunk 83 optimal weight: 0.0470 chunk 228 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 61 optimal weight: 0.0170 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 433 ASN E 76 GLN ** 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 = 0.3997 r_free = 0.3997 target = 0.164584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129297 restraints weight = 29907.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132602 restraints weight = 47446.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134625 restraints weight = 24258.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135413 restraints weight = 16954.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136512 restraints weight = 15086.041| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19087 Z= 0.098 Angle : 0.545 11.162 25945 Z= 0.258 Chirality : 0.039 0.166 3036 Planarity : 0.004 0.062 3249 Dihedral : 5.573 58.239 2991 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.55 % Allowed : 18.37 % Favored : 80.08 % 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: 0.78 (0.18), residues: 2322 helix: 1.89 (0.17), residues: 1032 sheet: 0.26 (0.28), residues: 345 loop : -0.94 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.016 0.001 TYR A 824 PHE 0.020 0.001 PHE A 675 TRP 0.012 0.001 TRP A 81 HIS 0.003 0.000 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00214 (19085) covalent geometry : angle 0.54494 (25939) hydrogen bonds : bond 0.03503 ( 892) hydrogen bonds : angle 3.95539 ( 2577) link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 0.69942 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.68 seconds wall clock time: 48 minutes 27.42 seconds (2907.42 seconds total)