Starting phenix.real_space_refine on Mon Jun 16 19:13:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.map" model { file = "/net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tvz_26142/06_2025/7tvz_26142.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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, 'ASN:plan1': 1, 'ASP:plan': 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: 11.92, per 1000 atoms: 0.64 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: 4.97 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.24 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: 7.04 Time building geometry restraints manager: 5.95 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 46.370 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (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 TRP 0.016 0.001 TRP B 723 HIS 0.003 0.000 HIS E 532 PHE 0.013 0.001 PHE E 79 TYR 0.013 0.001 TYR B 519 ARG 0.004 0.000 ARG E 427 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 2) link_NAG-ASN : angle 0.81205 ( 6) hydrogen bonds : bond 0.13921 ( 892) hydrogen bonds : angle 5.32074 ( 2577) covalent geometry : bond 0.00485 (19085) covalent geometry : angle 0.61121 (25939) *********************** 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 : 2.009 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: 0.7393 (mt) REVERT: E 157 GLU cc_start: 0.8358 (tp30) cc_final: 0.8108 (tp30) REVERT: E 309 ASN cc_start: 0.8052 (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: 0.3157 time to fit residues: 184.6468 Evaluate side-chains 181 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128293 restraints weight = 30044.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131256 restraints weight = 52215.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133931 restraints weight = 25716.549| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19087 Z= 0.226 Angle : 0.681 9.887 25945 Z= 0.331 Chirality : 0.045 0.208 3036 Planarity : 0.005 0.061 3249 Dihedral : 8.833 96.559 2991 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.10 % Allowed : 9.56 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2322 helix: 1.51 (0.17), residues: 1012 sheet: 0.25 (0.28), residues: 346 loop : -1.28 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 333 HIS 0.007 0.001 HIS B 98 PHE 0.022 0.002 PHE E 134 TYR 0.027 0.002 TYR A 824 ARG 0.010 0.001 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 2) link_NAG-ASN : angle 0.81238 ( 6) hydrogen bonds : bond 0.05775 ( 892) hydrogen bonds : angle 4.61994 ( 2577) covalent geometry : bond 0.00551 (19085) covalent geometry : angle 0.68104 (25939) *********************** 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: 42 poor density : 191 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7719 (ttp) cc_final: 0.7450 (ttt) REVERT: A 641 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8396 (m) REVERT: A 752 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: A 803 ILE cc_start: 0.8238 (mm) cc_final: 0.7604 (mt) REVERT: B 66 MET cc_start: 0.6532 (ptt) cc_final: 0.6226 (ptp) REVERT: E 81 ILE cc_start: 0.8794 (mp) cc_final: 0.8468 (mt) REVERT: E 157 GLU cc_start: 0.8528 (tp30) cc_final: 0.8230 (tp30) REVERT: E 308 TYR cc_start: 0.8534 (m-80) cc_final: 0.8267 (m-10) REVERT: E 674 GLN cc_start: 0.8873 (mp10) cc_final: 0.8582 (mt0) outliers start: 42 outliers final: 20 residues processed: 220 average time/residue: 0.3022 time to fit residues: 101.3917 Evaluate side-chains 179 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 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 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 219 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 52 optimal weight: 0.0870 chunk 143 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 209 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN B 593 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 = 0.4011 r_free = 0.4011 target = 0.166169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132288 restraints weight = 29814.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133549 restraints weight = 45873.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.135425 restraints weight = 31257.092| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19087 Z= 0.108 Angle : 0.553 9.397 25945 Z= 0.263 Chirality : 0.040 0.235 3036 Planarity : 0.004 0.059 3249 Dihedral : 7.337 68.930 2991 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.70 % Allowed : 11.26 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2322 helix: 1.77 (0.17), residues: 1024 sheet: 0.43 (0.28), residues: 342 loop : -1.10 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 94 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE B 511 TYR 0.021 0.001 TYR A 824 ARG 0.004 0.000 ARG E 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 2) link_NAG-ASN : angle 1.14224 ( 6) hydrogen bonds : bond 0.04132 ( 892) hydrogen bonds : angle 4.19133 ( 2577) covalent geometry : bond 0.00221 (19085) covalent geometry : angle 0.55260 (25939) *********************** 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 222 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.7828 (ttp) cc_final: 0.7518 (ttt) REVERT: A 309 HIS cc_start: 0.7452 (t-90) cc_final: 0.7102 (t70) REVERT: A 803 ILE cc_start: 0.8175 (mm) cc_final: 0.7507 (mt) REVERT: A 887 ASP cc_start: 0.7329 (t0) cc_final: 0.7044 (m-30) REVERT: B 435 MET cc_start: 0.7488 (mtt) cc_final: 0.7259 (mtt) REVERT: B 496 TRP cc_start: 0.7276 (m100) cc_final: 0.6874 (m100) REVERT: B 864 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7641 (tp) REVERT: E 81 ILE cc_start: 0.8750 (mp) cc_final: 0.8439 (mt) REVERT: E 157 GLU cc_start: 0.8410 (tp30) cc_final: 0.8126 (tp30) REVERT: E 308 TYR cc_start: 0.8383 (m-80) cc_final: 0.8036 (m-10) REVERT: E 674 GLN cc_start: 0.8738 (mp10) cc_final: 0.8129 (mt0) outliers start: 34 outliers final: 19 residues processed: 211 average time/residue: 0.2794 time to fit residues: 93.1817 Evaluate side-chains 186 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 28 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 112 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 151 optimal weight: 0.0370 chunk 214 optimal weight: 7.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119762 restraints weight = 30180.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118486 restraints weight = 36566.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114471 restraints weight = 21654.778| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19087 Z= 0.286 Angle : 0.720 11.825 25945 Z= 0.353 Chirality : 0.046 0.188 3036 Planarity : 0.006 0.067 3249 Dihedral : 6.963 59.396 2991 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.70 % Allowed : 13.66 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2322 helix: 1.31 (0.17), residues: 1017 sheet: 0.11 (0.28), residues: 341 loop : -1.32 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 333 HIS 0.007 0.002 HIS E 220 PHE 0.026 0.003 PHE A 114 TYR 0.023 0.003 TYR A 824 ARG 0.006 0.001 ARG B 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 2) link_NAG-ASN : angle 1.21478 ( 6) hydrogen bonds : bond 0.06595 ( 892) hydrogen bonds : angle 4.72435 ( 2577) covalent geometry : bond 0.00703 (19085) covalent geometry : angle 0.71948 (25939) *********************** 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: 54 poor density : 165 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.7716 (ttp) cc_final: 0.7441 (ttt) REVERT: A 96 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7567 (mtm110) REVERT: B 864 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7652 (tp) REVERT: E 81 ILE cc_start: 0.8900 (mp) cc_final: 0.8604 (mt) REVERT: E 308 TYR cc_start: 0.8736 (m-80) cc_final: 0.8489 (m-10) REVERT: E 309 ASN cc_start: 0.7854 (m-40) cc_final: 0.7550 (m-40) REVERT: E 549 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.6828 (m-80) REVERT: E 674 GLN cc_start: 0.9056 (mp10) cc_final: 0.8723 (mp10) outliers start: 54 outliers final: 32 residues processed: 208 average time/residue: 0.3841 time to fit residues: 125.7095 Evaluate side-chains 187 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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 546 ASP 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 B residue 55 HIS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 546 ASP 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 298 THR Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 549 PHE Chi-restraints excluded: chain E residue 639 PHE Chi-restraints excluded: chain E residue 641 SER 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 61 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 111 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.162068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126797 restraints weight = 29949.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129942 restraints weight = 48930.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131875 restraints weight = 24568.966| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19087 Z= 0.117 Angle : 0.557 9.996 25945 Z= 0.269 Chirality : 0.040 0.175 3036 Planarity : 0.004 0.064 3249 Dihedral : 6.538 56.135 2991 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.85 % Allowed : 15.62 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2322 helix: 1.67 (0.17), residues: 1017 sheet: 0.17 (0.28), residues: 350 loop : -1.16 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 81 HIS 0.005 0.001 HIS A 37 PHE 0.016 0.001 PHE B 511 TYR 0.020 0.001 TYR A 824 ARG 0.005 0.000 ARG A 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 0.94126 ( 6) hydrogen bonds : bond 0.04524 ( 892) hydrogen bonds : angle 4.28228 ( 2577) covalent geometry : bond 0.00261 (19085) covalent geometry : angle 0.55684 (25939) *********************** 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 209 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 2.616 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7498 (mtm110) REVERT: B 142 GLU cc_start: 0.8328 (tp30) cc_final: 0.8075 (tm-30) REVERT: B 186 GLN cc_start: 0.6212 (mm-40) cc_final: 0.5704 (tp40) REVERT: B 864 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7801 (tp) REVERT: E 81 ILE cc_start: 0.8864 (mp) cc_final: 0.8582 (mt) REVERT: E 308 TYR cc_start: 0.8616 (m-80) cc_final: 0.8346 (m-10) REVERT: E 674 GLN cc_start: 0.8916 (mp10) cc_final: 0.8671 (mp10) outliers start: 37 outliers final: 21 residues processed: 200 average time/residue: 0.3736 time to fit residues: 118.9518 Evaluate side-chains 182 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 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 498 ILE Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 89 TRP 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 480 LYS Chi-restraints excluded: chain E residue 639 PHE 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 26 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 GLN 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 = 0.3973 r_free = 0.3973 target = 0.162408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121331 restraints weight = 30116.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118774 restraints weight = 29148.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120145 restraints weight = 25411.737| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19087 Z= 0.120 Angle : 0.551 9.042 25945 Z= 0.264 Chirality : 0.040 0.171 3036 Planarity : 0.004 0.062 3249 Dihedral : 6.292 59.406 2991 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.80 % Allowed : 17.07 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2322 helix: 1.76 (0.17), residues: 1022 sheet: 0.27 (0.28), residues: 348 loop : -1.11 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 492 HIS 0.004 0.001 HIS A 37 PHE 0.016 0.001 PHE B 511 TYR 0.018 0.001 TYR A 824 ARG 0.004 0.000 ARG A 514 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 2) link_NAG-ASN : angle 0.96551 ( 6) hydrogen bonds : bond 0.04281 ( 892) hydrogen bonds : angle 4.14734 ( 2577) covalent geometry : bond 0.00279 (19085) covalent geometry : angle 0.55074 (25939) *********************** 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 203 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 3.084 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7506 (mtm110) REVERT: B 186 GLN cc_start: 0.6190 (mm-40) cc_final: 0.5572 (tp40) REVERT: B 496 TRP cc_start: 0.7065 (m100) cc_final: 0.6654 (m100) REVERT: B 864 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7601 (tp) REVERT: E 81 ILE cc_start: 0.8870 (mp) cc_final: 0.8592 (mt) REVERT: E 308 TYR cc_start: 0.8659 (m-80) cc_final: 0.8331 (m-10) REVERT: E 309 ASN cc_start: 0.7723 (m-40) cc_final: 0.7515 (m-40) REVERT: E 547 LEU cc_start: 0.8052 (tt) cc_final: 0.7742 (tt) REVERT: E 674 GLN cc_start: 0.8955 (mp10) cc_final: 0.8671 (mp10) outliers start: 36 outliers final: 25 residues processed: 195 average time/residue: 0.3749 time to fit residues: 115.1985 Evaluate side-chains 186 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER 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 864 ILE Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 89 TRP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 298 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 639 PHE Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 133 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 182 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 GLN B 163 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 = 0.3974 r_free = 0.3974 target = 0.162466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123779 restraints weight = 29896.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125009 restraints weight = 36820.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125182 restraints weight = 22671.677| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19087 Z= 0.121 Angle : 0.556 11.941 25945 Z= 0.266 Chirality : 0.040 0.170 3036 Planarity : 0.004 0.060 3249 Dihedral : 6.155 59.811 2991 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.95 % Allowed : 17.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2322 helix: 1.76 (0.17), residues: 1029 sheet: 0.27 (0.28), residues: 343 loop : -1.09 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 492 HIS 0.004 0.001 HIS A 37 PHE 0.015 0.001 PHE B 659 TYR 0.016 0.001 TYR A 824 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 0.87292 ( 6) hydrogen bonds : bond 0.04160 ( 892) hydrogen bonds : angle 4.11243 ( 2577) covalent geometry : bond 0.00284 (19085) covalent geometry : angle 0.55557 (25939) *********************** 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 210 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7516 (mtm110) REVERT: A 433 ASN cc_start: 0.7549 (t0) cc_final: 0.7278 (t0) REVERT: B 186 GLN cc_start: 0.5934 (mm-40) cc_final: 0.5499 (tp40) REVERT: B 496 TRP cc_start: 0.7016 (m100) cc_final: 0.6656 (m100) REVERT: B 719 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: B 864 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7665 (tp) REVERT: E 81 ILE cc_start: 0.8845 (mp) cc_final: 0.8552 (mt) REVERT: E 308 TYR cc_start: 0.8629 (m-80) cc_final: 0.8357 (m-10) REVERT: E 547 LEU cc_start: 0.8188 (tt) cc_final: 0.7921 (tt) REVERT: E 549 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: E 648 MET cc_start: 0.7623 (tmm) cc_final: 0.7064 (tmm) REVERT: E 674 GLN cc_start: 0.8971 (mp10) cc_final: 0.8665 (mp10) outliers start: 39 outliers final: 26 residues processed: 201 average time/residue: 0.2990 time to fit residues: 95.3845 Evaluate side-chains 190 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 719 PHE 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 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 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 14 optimal weight: 6.9990 chunk 142 optimal weight: 0.0010 chunk 178 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 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 = 0.3963 r_free = 0.3963 target = 0.161599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121772 restraints weight = 29813.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122761 restraints weight = 36087.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123655 restraints weight = 24153.777| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19087 Z= 0.131 Angle : 0.561 11.367 25945 Z= 0.269 Chirality : 0.040 0.171 3036 Planarity : 0.004 0.060 3249 Dihedral : 6.049 55.985 2991 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.05 % Allowed : 16.92 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2322 helix: 1.75 (0.17), residues: 1029 sheet: 0.25 (0.28), residues: 343 loop : -1.09 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 831 HIS 0.004 0.001 HIS A 37 PHE 0.021 0.001 PHE B 511 TYR 0.018 0.001 TYR A 824 ARG 0.002 0.000 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00226 ( 2) link_NAG-ASN : angle 0.92448 ( 6) hydrogen bonds : bond 0.04315 ( 892) hydrogen bonds : angle 4.13659 ( 2577) covalent geometry : bond 0.00312 (19085) covalent geometry : angle 0.56083 (25939) *********************** 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 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 2.058 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7494 (mtm110) REVERT: A 288 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (tt) REVERT: B 186 GLN cc_start: 0.5911 (mm-40) cc_final: 0.5501 (tp40) REVERT: B 496 TRP cc_start: 0.6914 (m100) cc_final: 0.6530 (m100) REVERT: B 719 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: B 864 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7706 (tp) REVERT: E 81 ILE cc_start: 0.8866 (mp) cc_final: 0.8589 (mt) REVERT: E 308 TYR cc_start: 0.8686 (m-80) cc_final: 0.8463 (m-10) REVERT: E 547 LEU cc_start: 0.8212 (tt) cc_final: 0.7969 (tt) REVERT: E 549 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: E 648 MET cc_start: 0.7609 (tmm) cc_final: 0.7083 (tmm) REVERT: E 674 GLN cc_start: 0.9018 (mp10) cc_final: 0.8721 (mp10) outliers start: 41 outliers final: 27 residues processed: 195 average time/residue: 0.2806 time to fit residues: 87.4071 Evaluate side-chains 187 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 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 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 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 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 69 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 223 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125044 restraints weight = 30053.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128871 restraints weight = 51965.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.130962 restraints weight = 23018.003| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3522 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= 0.170 Angle : 0.601 10.734 25945 Z= 0.289 Chirality : 0.041 0.176 3036 Planarity : 0.005 0.059 3249 Dihedral : 6.064 55.589 2991 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 17.07 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2322 helix: 1.65 (0.17), residues: 1027 sheet: 0.16 (0.28), residues: 343 loop : -1.16 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 831 HIS 0.004 0.001 HIS E 220 PHE 0.020 0.002 PHE B 675 TYR 0.020 0.002 TYR A 824 ARG 0.003 0.000 ARG B 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 2) link_NAG-ASN : angle 0.98453 ( 6) hydrogen bonds : bond 0.04859 ( 892) hydrogen bonds : angle 4.24900 ( 2577) covalent geometry : bond 0.00415 (19085) covalent geometry : angle 0.60129 (25939) *********************** 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 202 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7471 (mtm110) REVERT: A 433 ASN cc_start: 0.7568 (t0) cc_final: 0.7328 (t0) REVERT: A 675 PHE cc_start: 0.7668 (t80) cc_final: 0.7461 (t80) REVERT: B 186 GLN cc_start: 0.6074 (mm-40) cc_final: 0.5566 (tp40) REVERT: B 496 TRP cc_start: 0.6979 (m100) cc_final: 0.6633 (m100) REVERT: B 719 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: B 864 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7785 (tp) REVERT: E 81 ILE cc_start: 0.8884 (mp) cc_final: 0.8597 (mt) REVERT: E 308 TYR cc_start: 0.8758 (m-80) cc_final: 0.8509 (m-10) REVERT: E 547 LEU cc_start: 0.8146 (tt) cc_final: 0.7881 (tt) REVERT: E 549 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: E 674 GLN cc_start: 0.8966 (mp10) cc_final: 0.8694 (mp10) outliers start: 42 outliers final: 32 residues processed: 194 average time/residue: 0.2851 time to fit residues: 87.8224 Evaluate side-chains 189 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 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 120 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 SER 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 831 TRP 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 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 667 GLU Chi-restraints excluded: chain E residue 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 120 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 135 optimal weight: 0.0670 chunk 117 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 171 optimal weight: 0.0970 chunk 90 optimal weight: 0.7980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.163412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124586 restraints weight = 29903.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126557 restraints weight = 36090.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124778 restraints weight = 21227.021| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19087 Z= 0.101 Angle : 0.547 10.618 25945 Z= 0.261 Chirality : 0.039 0.169 3036 Planarity : 0.004 0.061 3249 Dihedral : 5.780 57.461 2991 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.30 % Allowed : 18.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2322 helix: 1.85 (0.17), residues: 1029 sheet: 0.23 (0.28), residues: 343 loop : -1.05 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.004 0.000 HIS A 37 PHE 0.020 0.001 PHE B 511 TYR 0.017 0.001 TYR A 824 ARG 0.002 0.000 ARG E 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 2) link_NAG-ASN : angle 0.88715 ( 6) hydrogen bonds : bond 0.03807 ( 892) hydrogen bonds : angle 4.05011 ( 2577) covalent geometry : bond 0.00217 (19085) covalent geometry : angle 0.54720 (25939) ********************** 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 189 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 2.184 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7458 (mtm110) REVERT: A 433 ASN cc_start: 0.7551 (t0) cc_final: 0.7315 (t0) REVERT: A 719 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5234 (m-80) REVERT: B 186 GLN cc_start: 0.5905 (mm-40) cc_final: 0.5528 (tp40) REVERT: B 496 TRP cc_start: 0.7120 (m100) cc_final: 0.6658 (m100) REVERT: B 719 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: B 741 MET cc_start: 0.6788 (tmm) cc_final: 0.5895 (tpp) REVERT: E 81 ILE cc_start: 0.8811 (mp) cc_final: 0.8556 (mt) REVERT: E 308 TYR cc_start: 0.8691 (m-80) cc_final: 0.8489 (m-10) REVERT: E 547 LEU cc_start: 0.8322 (tt) cc_final: 0.8049 (tt) REVERT: E 549 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: E 648 MET cc_start: 0.7497 (tmm) cc_final: 0.6838 (tmm) REVERT: E 674 GLN cc_start: 0.9002 (mp10) cc_final: 0.8691 (mp10) outliers start: 26 outliers final: 22 residues processed: 184 average time/residue: 0.2884 time to fit residues: 83.9348 Evaluate side-chains 180 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 719 PHE Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 842 ILE 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 677 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 231 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 115 optimal weight: 0.0570 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.161567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126457 restraints weight = 30016.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129754 restraints weight = 51713.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.131775 restraints weight = 24389.531| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19087 Z= 0.136 Angle : 0.573 11.240 25945 Z= 0.273 Chirality : 0.040 0.170 3036 Planarity : 0.004 0.060 3249 Dihedral : 5.754 56.628 2991 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.65 % Allowed : 17.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2322 helix: 1.80 (0.17), residues: 1028 sheet: 0.19 (0.28), residues: 343 loop : -1.07 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 831 HIS 0.004 0.001 HIS A 37 PHE 0.032 0.001 PHE A 294 TYR 0.019 0.001 TYR A 824 ARG 0.003 0.000 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 2) link_NAG-ASN : angle 0.89397 ( 6) hydrogen bonds : bond 0.04252 ( 892) hydrogen bonds : angle 4.10567 ( 2577) covalent geometry : bond 0.00327 (19085) covalent geometry : angle 0.57271 (25939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.22 seconds wall clock time: 105 minutes 34.60 seconds (6334.60 seconds total)