Starting phenix.real_space_refine on Sun Sep 13 06:43:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.cif" model { file = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jzo_9898/09_2026/6jzo_9898.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 4 4.78 5 C 14037 2.51 5 N 3524 2.21 5 O 3748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21405 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5296 Classifications: {'peptide': 668} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 26, 'TRANS': 641} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 24, 'TRANS': 638} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5266 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 24, 'TRANS': 638} Chain breaks: 6 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5255 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 24, 'TRANS': 638} Chain breaks: 6 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 4, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {' NA': 1, 'LPP': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' NA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' NA': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.08, per 1000 atoms: 0.24 Number of scatterers: 21405 At special positions: 0 Unit cell: (136.53, 136.53, 134.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Na 4 11.00 O 3748 8.00 N 3524 7.00 C 14037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=1.87 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=1.53 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.26 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " distance=1.30 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 890.5 milliseconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5106 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 72.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.750A pdb=" N VAL A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.847A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.559A pdb=" N ILE A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.808A pdb=" N LYS A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 removed outlier: 3.769A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.508A pdb=" N LEU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.575A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.747A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.617A pdb=" N LEU A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 339 through 346 removed outlier: 3.649A pdb=" N CYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 361 through 384 removed outlier: 4.116A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.798A pdb=" N TRP A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.930A pdb=" N ASP A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 457 removed outlier: 3.769A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 490 Processing helix chain 'A' and resid 491 through 499 removed outlier: 4.153A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 498 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 542 removed outlier: 3.640A pdb=" N GLN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 542 " --> pdb=" O TYR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.569A pdb=" N VAL A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 612 through 628 Processing helix chain 'A' and resid 631 through 644 removed outlier: 3.930A pdb=" N PHE A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 693 through 727 removed outlier: 3.605A pdb=" N LYS A 726 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 727 " --> pdb=" O ARG A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 755 removed outlier: 4.243A pdb=" N VAL A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.559A pdb=" N ILE B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 removed outlier: 3.808A pdb=" N LYS B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.769A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 removed outlier: 3.507A pdb=" N LEU B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.575A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.687A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 305 through 315 removed outlier: 3.656A pdb=" N LEU B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.504A pdb=" N ARG B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.649A pdb=" N CYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 361 through 384 removed outlier: 4.116A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 422 removed outlier: 3.799A pdb=" N TRP B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.930A pdb=" N ASP B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 457 removed outlier: 3.769A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 Processing helix chain 'B' and resid 491 through 499 removed outlier: 4.153A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 542 removed outlier: 3.649A pdb=" N GLN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 519 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 523 " --> pdb=" O PHE B 519 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR B 540 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 542 " --> pdb=" O TYR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.637A pdb=" N VAL B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 612 through 629 removed outlier: 3.992A pdb=" N ASP B 629 " --> pdb=" O GLN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 644 removed outlier: 3.528A pdb=" N ALA B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 693 through 727 removed outlier: 3.826A pdb=" N LYS B 726 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 755 removed outlier: 4.242A pdb=" N VAL B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 746 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 72 through 80 removed outlier: 3.791A pdb=" N ALA C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.559A pdb=" N ILE C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 removed outlier: 3.808A pdb=" N LYS C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 116 removed outlier: 3.769A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 removed outlier: 3.508A pdb=" N LEU C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.575A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.676A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.656A pdb=" N LEU C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.504A pdb=" N ARG C 323 " --> pdb=" O GLY C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.649A pdb=" N CYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 361 through 384 removed outlier: 4.116A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 422 removed outlier: 3.799A pdb=" N TRP C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 424 through 432 removed outlier: 3.930A pdb=" N ASP C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 457 removed outlier: 3.769A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 490 Processing helix chain 'C' and resid 491 through 499 removed outlier: 4.153A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 498 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 542 removed outlier: 3.649A pdb=" N GLN C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 519 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU C 542 " --> pdb=" O TYR C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 611 through 628 Processing helix chain 'C' and resid 630 through 644 removed outlier: 3.528A pdb=" N ALA C 638 " --> pdb=" O GLU C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 693 through 727 removed outlier: 3.830A pdb=" N LYS C 726 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 727 " --> pdb=" O ARG C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 755 removed outlier: 4.242A pdb=" N VAL C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 741 " --> pdb=" O LYS C 737 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 746 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 752 " --> pdb=" O PHE C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.693A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.558A pdb=" N ILE D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 removed outlier: 3.808A pdb=" N LYS D 106 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 removed outlier: 3.769A pdb=" N LEU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 removed outlier: 3.507A pdb=" N LEU D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.575A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.844A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.828A pdb=" N LEU D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 305 through 315 removed outlier: 3.657A pdb=" N LEU D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 3.504A pdb=" N ARG D 323 " --> pdb=" O GLY D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.649A pdb=" N CYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 361 through 384 removed outlier: 4.116A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 removed outlier: 3.799A pdb=" N TRP D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.930A pdb=" N ASP D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 457 removed outlier: 3.768A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 491 through 499 removed outlier: 4.153A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 498 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 542 removed outlier: 3.649A pdb=" N GLN D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 519 " --> pdb=" O ASP D 515 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 523 " --> pdb=" O PHE D 519 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR D 540 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU D 542 " --> pdb=" O TYR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.535A pdb=" N VAL D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 611 through 628 Processing helix chain 'D' and resid 630 through 644 removed outlier: 3.700A pdb=" N PHE D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 638 " --> pdb=" O GLU D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 693 through 727 removed outlier: 3.873A pdb=" N LYS D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR D 727 " --> pdb=" O ARG D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 755 removed outlier: 4.243A pdb=" N VAL D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN D 741 " --> pdb=" O LYS D 737 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE D 746 " --> pdb=" O ASP D 742 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 169 removed outlier: 3.709A pdb=" N VAL A 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.540A pdb=" N VAL C 168 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.546A pdb=" N VAL D 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) 1277 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5677 1.33 - 1.45: 4169 1.45 - 1.57: 11909 1.57 - 1.69: 4 1.69 - 1.81: 140 Bond restraints: 21899 Sorted by residual: bond pdb=" O5 LPP A 803 " pdb=" P1 LPP A 803 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP D 802 " pdb=" P1 LPP D 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP A 802 " pdb=" P1 LPP A 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O5 LPP C 802 " pdb=" P1 LPP C 802 " ideal model delta sigma weight residual 2.278 1.603 0.675 2.00e-02 2.50e+03 1.14e+03 bond pdb=" O4 LPP C 802 " pdb=" P1 LPP C 802 " ideal model delta sigma weight residual 1.764 1.508 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 21894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.20: 29620 8.20 - 16.40: 69 16.40 - 24.60: 5 24.60 - 32.80: 4 32.80 - 41.00: 8 Bond angle restraints: 29706 Sorted by residual: angle pdb=" O4 LPP A 803 " pdb=" P1 LPP A 803 " pdb=" O5 LPP A 803 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP C 802 " pdb=" P1 LPP C 802 " pdb=" O5 LPP C 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP D 802 " pdb=" P1 LPP D 802 " pdb=" O5 LPP D 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" O4 LPP A 802 " pdb=" P1 LPP A 802 " pdb=" O5 LPP A 802 " ideal model delta sigma weight residual 62.99 103.99 -41.00 3.00e+00 1.11e-01 1.87e+02 angle pdb=" C6 LPP D 802 " pdb=" O5 LPP D 802 " pdb=" P1 LPP D 802 " ideal model delta sigma weight residual 82.33 121.49 -39.16 3.00e+00 1.11e-01 1.70e+02 ... (remaining 29701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.36: 12257 20.36 - 40.72: 573 40.72 - 61.08: 175 61.08 - 81.44: 22 81.44 - 101.80: 5 Dihedral angle restraints: 13032 sinusoidal: 5205 harmonic: 7827 Sorted by residual: dihedral pdb=" CB CYS A 549 " pdb=" SG CYS A 549 " pdb=" SG CYS A 554 " pdb=" CB CYS A 554 " ideal model delta sinusoidal sigma weight residual -86.00 0.72 -86.72 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS B 549 " pdb=" SG CYS B 549 " pdb=" SG CYS B 554 " pdb=" CB CYS B 554 " ideal model delta sinusoidal sigma weight residual -86.00 -21.26 -64.74 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA PRO C 398 " pdb=" C PRO C 398 " pdb=" N PRO C 399 " pdb=" CA PRO C 399 " ideal model delta harmonic sigma weight residual -180.00 -144.14 -35.86 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 13029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3019 0.103 - 0.206: 292 0.206 - 0.309: 51 0.309 - 0.413: 17 0.413 - 0.516: 14 Chirality restraints: 3393 Sorted by residual: chirality pdb=" CA LYS C 60 " pdb=" N LYS C 60 " pdb=" C LYS C 60 " pdb=" CB LYS C 60 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CBH Y01 B 801 " pdb=" CAT Y01 B 801 " pdb=" CAZ Y01 B 801 " pdb=" CBF Y01 B 801 " both_signs ideal model delta sigma weight residual False -2.85 -2.37 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CBH Y01 A 801 " pdb=" CAT Y01 A 801 " pdb=" CAZ Y01 A 801 " pdb=" CBF Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.85 -2.37 -0.48 2.00e-01 2.50e+01 5.72e+00 ... (remaining 3390 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 396 " 0.087 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO A 397 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 397 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 397 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 655 " 0.092 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO A 656 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 350 " 0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO D 351 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 351 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 351 " 0.048 5.00e-02 4.00e+02 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 19 2.08 - 2.79: 5575 2.79 - 3.49: 27942 3.49 - 4.20: 50114 4.20 - 4.90: 89155 Nonbonded interactions: 172805 Sorted by model distance: nonbonded pdb=" CD PRO A 216 " pdb=" CE MET A 710 " model vdw 1.379 3.860 nonbonded pdb=" NH1 ARG B 71 " pdb=" OE1 GLU B 79 " model vdw 1.447 3.120 nonbonded pdb=" NH2 ARG D 196 " pdb=" OE2 GLU D 234 " model vdw 1.568 3.120 nonbonded pdb=" CD PRO B 216 " pdb=" CE MET B 710 " model vdw 1.618 3.860 nonbonded pdb=" O SER A 467 " pdb=" CD1 TRP A 468 " model vdw 1.841 3.260 ... (remaining 172800 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 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 71 or (resid 72 through 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 115 or (re \ sid 116 through 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 398 or (resid 399 and (name N or name CA or name C or name O o \ r name CB )) or resid 400 through 468 or (resid 469 and (name N or name CA or na \ me C or name O or name CB )) or resid 470 through 477 or (resid 478 through 479 \ and (name N or name CA or name C or name O or name CB )) or resid 480 through 54 \ 3 or (resid 544 through 545 and (name N or name CA or name C or name O or name C \ B )) or resid 546 through 557 or (resid 558 and (name N or name CA or name C or \ name O or name CB )) or resid 559 through 651 or (resid 652 through 653 and (nam \ e N or name CA or name C or name O or name CB )) or resid 654 through 655 or (re \ sid 656 and (name N or name CA or name C or name O or name CB )) or resid 657 th \ rough 660 or resid 692 through 801)) selection = (chain 'B' and (resid 15 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 71 or (resid 72 throu \ gh 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throu \ gh 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or \ resid 431 through 468 or (resid 469 and (name N or name CA or name C or name O \ or name CB )) or resid 470 through 477 or (resid 478 through 479 and (name N or \ name CA or name C or name O or name CB )) or resid 480 through 543 or (resid 544 \ through 545 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 46 through 557 or (resid 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 659 or (resid 660 and (name N or name CA or name C or \ name O or name CB )) or resid 692 through 801)) selection = (chain 'C' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 71 or (resid 72 through 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 115 or (re \ sid 116 through 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 398 or (resid 399 and (name N or name CA or name C or name O o \ r name CB )) or resid 400 through 468 or (resid 469 and (name N or name CA or na \ me C or name O or name CB )) or resid 470 through 477 or (resid 478 through 479 \ and (name N or name CA or name C or name O or name CB )) or resid 480 through 55 \ 7 or (resid 558 and (name N or name CA or name C or name O or name CB )) or resi \ d 559 through 655 or (resid 656 and (name N or name CA or name C or name O or na \ me CB )) or resid 657 through 659 or (resid 660 and (name N or name CA or name C \ or name O or name CB )) or resid 692 through 801)) selection = (chain 'D' and (resid 15 through 115 or (resid 116 through 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 398 or (resid 399 a \ nd (name N or name CA or name C or name O or name CB )) or resid 400 through 543 \ or (resid 544 through 545 and (name N or name CA or name C or name O or name CB \ )) or resid 546 through 652 or (resid 653 and (name N or name CA or name C or n \ ame O or name CB )) or resid 654 through 655 or (resid 656 and (name N or name C \ A or name C or name O or name CB )) or resid 657 through 659 or (resid 660 and ( \ name N or name CA or name C or name O or name CB )) or resid 692 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.016 0.728 21906 Z= 0.913 Angle : 1.474 42.093 29714 Z= 0.777 Chirality : 0.077 0.516 3393 Planarity : 0.008 0.134 3668 Dihedral : 13.597 101.803 7914 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 2.65 % Favored : 96.89 % Rotamer: Outliers : 3.26 % Allowed : 3.99 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.11), residues: 2601 helix: -3.09 (0.08), residues: 1786 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 716 TYR 0.024 0.003 TYR A 523 PHE 0.031 0.004 PHE A 539 TRP 0.032 0.002 TRP D 409 HIS 0.004 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.01328 / 0.65 (21899) covalent geometry : angle 1.44049 / 0.76 (29706) SS BOND : bond 0.46381 / 22.91 ( 4) SS BOND : angle 19.11162 / 9.40 ( 8) hydrogen bonds : bond 0.16674 / 11.16 ( 1277) hydrogen bonds : angle 8.77794 / 6.18 ( 3720) Misc. bond : bond 0.47397 / 23.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 635 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: A 140 THR cc_start: 0.9026 (m) cc_final: 0.8776 (p) REVERT: A 254 ASP cc_start: 0.8154 (m-30) cc_final: 0.7815 (m-30) REVERT: A 257 ASP cc_start: 0.7927 (m-30) cc_final: 0.7694 (m-30) REVERT: A 339 LEU cc_start: 0.9027 (mt) cc_final: 0.8728 (mt) REVERT: A 359 ILE cc_start: 0.9002 (tt) cc_final: 0.8689 (tt) REVERT: A 419 LYS cc_start: 0.8887 (tptm) cc_final: 0.8510 (tptp) REVERT: A 471 TRP cc_start: 0.8602 (m100) cc_final: 0.8238 (m-10) REVERT: A 505 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8138 (tp) REVERT: A 506 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: A 515 ASP cc_start: 0.7742 (m-30) cc_final: 0.7523 (m-30) REVERT: A 538 TYR cc_start: 0.8667 (m-80) cc_final: 0.8455 (m-80) REVERT: A 566 GLU cc_start: 0.8119 (tp30) cc_final: 0.7716 (mm-30) REVERT: A 615 MET cc_start: 0.7752 (mtt) cc_final: 0.7390 (mtt) REVERT: A 702 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7995 (mtm110) REVERT: A 703 HIS cc_start: 0.7936 (t70) cc_final: 0.7735 (t70) REVERT: A 708 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: A 721 MET cc_start: 0.8259 (mmp) cc_final: 0.7968 (mmp) REVERT: A 751 LEU cc_start: 0.8942 (mt) cc_final: 0.8467 (mt) REVERT: B 42 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8124 (mptt) REVERT: B 63 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8018 (pt) REVERT: B 92 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: B 242 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6993 (mt-10) REVERT: B 271 TYR cc_start: 0.9021 (t80) cc_final: 0.8549 (t80) REVERT: B 288 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6901 (mpt180) REVERT: B 339 LEU cc_start: 0.8922 (mt) cc_final: 0.8628 (mt) REVERT: B 358 PHE cc_start: 0.8754 (t80) cc_final: 0.8541 (t80) REVERT: B 359 ILE cc_start: 0.8978 (tt) cc_final: 0.8765 (tt) REVERT: B 405 MET cc_start: 0.6962 (mtp) cc_final: 0.6490 (mtp) REVERT: B 409 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7304 (m-90) REVERT: B 419 LYS cc_start: 0.8805 (tptm) cc_final: 0.8530 (tptp) REVERT: B 453 ILE cc_start: 0.7489 (mm) cc_final: 0.7084 (mm) REVERT: B 456 PHE cc_start: 0.7276 (t80) cc_final: 0.7061 (t80) REVERT: B 471 TRP cc_start: 0.8702 (m100) cc_final: 0.8489 (m100) REVERT: B 532 ASN cc_start: 0.7525 (m-40) cc_final: 0.7006 (m-40) REVERT: B 556 LYS cc_start: 0.7701 (tppt) cc_final: 0.7457 (tptp) REVERT: B 563 THR cc_start: 0.8629 (p) cc_final: 0.8223 (t) REVERT: B 619 MET cc_start: 0.8046 (ttm) cc_final: 0.7662 (ttp) REVERT: B 737 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7172 (mmmm) REVERT: B 740 LYS cc_start: 0.8272 (tttm) cc_final: 0.7961 (mtpp) REVERT: C 34 LYS cc_start: 0.8312 (mttt) cc_final: 0.8046 (mmtt) REVERT: C 81 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6873 (tm-30) REVERT: C 92 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: C 339 LEU cc_start: 0.9071 (mt) cc_final: 0.8838 (mp) REVERT: C 359 ILE cc_start: 0.8768 (tt) cc_final: 0.8525 (tt) REVERT: C 405 MET cc_start: 0.7038 (mtp) cc_final: 0.6609 (mtp) REVERT: C 409 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7418 (m-90) REVERT: C 419 LYS cc_start: 0.8890 (tptm) cc_final: 0.8574 (tptp) REVERT: C 453 ILE cc_start: 0.7589 (mm) cc_final: 0.7210 (mm) REVERT: C 456 PHE cc_start: 0.6995 (t80) cc_final: 0.6679 (t80) REVERT: C 466 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7460 (pp20) REVERT: C 505 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 532 ASN cc_start: 0.7744 (m-40) cc_final: 0.7463 (m-40) REVERT: C 563 THR cc_start: 0.8601 (p) cc_final: 0.8327 (t) REVERT: C 615 MET cc_start: 0.8079 (mtt) cc_final: 0.7876 (mtt) REVERT: C 703 HIS cc_start: 0.7648 (t70) cc_final: 0.7433 (t70) REVERT: C 737 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7429 (mmmm) REVERT: D 92 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6927 (m-80) REVERT: D 95 TYR cc_start: 0.8494 (t80) cc_final: 0.8235 (t80) REVERT: D 294 LYS cc_start: 0.8351 (tttm) cc_final: 0.8128 (tmtt) REVERT: D 359 ILE cc_start: 0.8776 (tt) cc_final: 0.8521 (tt) REVERT: D 419 LYS cc_start: 0.8834 (tptm) cc_final: 0.8528 (tptp) REVERT: D 453 ILE cc_start: 0.7621 (mm) cc_final: 0.7265 (mm) REVERT: D 456 PHE cc_start: 0.7002 (t80) cc_final: 0.6739 (t80) REVERT: D 466 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: D 505 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8212 (tp) REVERT: D 532 ASN cc_start: 0.7829 (m-40) cc_final: 0.7311 (m-40) REVERT: D 536 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8319 (tp40) REVERT: D 615 MET cc_start: 0.7969 (mtt) cc_final: 0.7747 (mtt) REVERT: D 619 MET cc_start: 0.7980 (ttm) cc_final: 0.7583 (ttp) REVERT: D 703 HIS cc_start: 0.7763 (t70) cc_final: 0.7318 (t-90) REVERT: D 737 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7262 (mmmm) REVERT: D 748 PHE cc_start: 0.8342 (m-80) cc_final: 0.8086 (m-80) outliers start: 72 outliers final: 26 residues processed: 697 average time/residue: 0.1740 time to fit residues: 180.9479 Evaluate side-chains 460 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 418 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 702 ARG Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 733 GLU Chi-restraints excluded: chain A residue 740 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 313 ARG Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 580 ASN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain C residue 92 PHE Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 580 ASN Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 466 GLU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 580 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 102 HIS A 154 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 HIS A 442 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 535 ASN A 536 GLN A 559 ASN A 580 ASN A 585 ASN A 622 ASN A 625 GLN A 735 ASN A 741 GLN B 80 ASN B 102 HIS B 154 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 HIS B 420 GLN B 442 ASN ** B 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN B 580 ASN B 622 ASN B 625 GLN B 704 HIS B 741 GLN C 102 HIS ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 HIS C 442 ASN C 472 HIS ** C 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 ASN C 622 ASN C 625 GLN C 704 HIS C 741 GLN D 102 HIS D 118 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 GLN D 369 HIS D 386 HIS D 442 ASN D 472 HIS D 535 ASN D 559 ASN D 580 ASN D 622 ASN D 625 GLN D 704 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.141394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.111796 restraints weight = 28449.303| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.00 r_work: 0.3063 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21906 Z= 0.148 Angle : 0.614 8.839 29714 Z= 0.320 Chirality : 0.042 0.229 3393 Planarity : 0.005 0.059 3668 Dihedral : 11.842 117.590 3179 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.49 % Allowed : 11.19 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 2601 helix: -0.80 (0.11), residues: 1867 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 71 TYR 0.023 0.001 TYR A 523 PHE 0.029 0.002 PHE B 378 TRP 0.017 0.001 TRP B 314 HIS 0.003 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (21899) covalent geometry : angle 0.61318 / 0.32 (29706) SS BOND : bond 0.01031 / 0.53 ( 4) SS BOND : angle 1.91880 / 1.16 ( 8) hydrogen bonds : bond 0.04384 / 2.91 ( 1277) hydrogen bonds : angle 4.41332 / 3.12 ( 3720) Misc. bond : bond 0.00272 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 481 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8786 (m-30) cc_final: 0.8582 (m-30) REVERT: A 257 ASP cc_start: 0.8267 (m-30) cc_final: 0.8028 (m-30) REVERT: A 323 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7085 (tpt170) REVERT: A 505 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 556 LYS cc_start: 0.8669 (tptt) cc_final: 0.8120 (tptp) REVERT: A 615 MET cc_start: 0.8730 (mtt) cc_final: 0.8488 (mtt) REVERT: A 619 MET cc_start: 0.8993 (ttp) cc_final: 0.8657 (ttp) REVERT: B 50 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7886 (mmtm) REVERT: B 79 GLU cc_start: 0.8297 (tt0) cc_final: 0.8057 (tt0) REVERT: B 246 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8137 (ttp-110) REVERT: B 272 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7624 (ttp80) REVERT: B 339 LEU cc_start: 0.8697 (mt) cc_final: 0.8378 (mt) REVERT: B 405 MET cc_start: 0.7355 (mtp) cc_final: 0.6591 (mtp) REVERT: B 409 TRP cc_start: 0.8621 (OUTLIER) cc_final: 0.7333 (m-90) REVERT: B 453 ILE cc_start: 0.8080 (mm) cc_final: 0.7732 (mm) REVERT: B 456 PHE cc_start: 0.7972 (t80) cc_final: 0.7613 (t80) REVERT: B 471 TRP cc_start: 0.8639 (m100) cc_final: 0.8109 (m-10) REVERT: B 532 ASN cc_start: 0.8672 (m-40) cc_final: 0.8364 (m-40) REVERT: B 563 THR cc_start: 0.8909 (p) cc_final: 0.8678 (t) REVERT: B 619 MET cc_start: 0.9087 (ttm) cc_final: 0.8793 (ttp) REVERT: B 621 ASN cc_start: 0.8593 (m110) cc_final: 0.8206 (m-40) REVERT: B 634 GLU cc_start: 0.8374 (tt0) cc_final: 0.7969 (mt-10) REVERT: B 737 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7534 (mmmt) REVERT: C 34 LYS cc_start: 0.8499 (mttt) cc_final: 0.7908 (mmtt) REVERT: C 228 GLN cc_start: 0.8122 (tp40) cc_final: 0.7903 (mm-40) REVERT: C 272 ARG cc_start: 0.7142 (ttp80) cc_final: 0.6636 (ttp80) REVERT: C 405 MET cc_start: 0.7450 (mtp) cc_final: 0.6525 (mtp) REVERT: C 409 TRP cc_start: 0.8588 (OUTLIER) cc_final: 0.7413 (m-90) REVERT: C 453 ILE cc_start: 0.8152 (mm) cc_final: 0.7765 (mm) REVERT: C 505 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8486 (tp) REVERT: C 532 ASN cc_start: 0.8715 (m-40) cc_final: 0.8481 (m-40) REVERT: C 563 THR cc_start: 0.8930 (p) cc_final: 0.8591 (t) REVERT: C 583 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8991 (t) REVERT: C 615 MET cc_start: 0.8855 (mtt) cc_final: 0.8614 (mtt) REVERT: C 737 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7703 (mmmm) REVERT: D 272 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6680 (ttp80) REVERT: D 294 LYS cc_start: 0.8724 (tttm) cc_final: 0.8327 (tmtt) REVERT: D 405 MET cc_start: 0.7276 (mtp) cc_final: 0.6964 (mtp) REVERT: D 419 LYS cc_start: 0.8543 (tptm) cc_final: 0.8269 (ttmt) REVERT: D 532 ASN cc_start: 0.8874 (m-40) cc_final: 0.8463 (m-40) REVERT: D 619 MET cc_start: 0.9043 (ttm) cc_final: 0.8767 (ttp) REVERT: D 634 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: D 703 HIS cc_start: 0.7825 (t70) cc_final: 0.7587 (t70) REVERT: D 737 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7596 (mmmm) outliers start: 77 outliers final: 41 residues processed: 539 average time/residue: 0.1464 time to fit residues: 124.0866 Evaluate side-chains 437 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 549 CYS Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 104 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.0370 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 472 HIS ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 GLN C 154 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN C 558 ASN ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 741 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.107693 restraints weight = 28323.568| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.05 r_work: 0.3015 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21906 Z= 0.145 Angle : 0.565 9.299 29714 Z= 0.292 Chirality : 0.042 0.287 3393 Planarity : 0.004 0.054 3668 Dihedral : 10.627 116.537 3103 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.89 % Allowed : 13.41 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2601 helix: 0.40 (0.12), residues: 1868 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 296 TYR 0.022 0.001 TYR A 523 PHE 0.022 0.002 PHE B 340 TRP 0.015 0.001 TRP B 314 HIS 0.002 0.001 HIS C 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (21899) covalent geometry : angle 0.56428 / 0.29 (29706) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 1.65360 / 1.29 ( 8) hydrogen bonds : bond 0.04067 / 2.70 ( 1277) hydrogen bonds : angle 3.90104 / 2.77 ( 3720) Misc. bond : bond 0.00299 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 432 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8300 (pt) REVERT: A 254 ASP cc_start: 0.8761 (m-30) cc_final: 0.8528 (m-30) REVERT: A 323 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7190 (tpt170) REVERT: A 419 LYS cc_start: 0.8650 (tptm) cc_final: 0.8422 (ttmt) REVERT: A 420 GLN cc_start: 0.7969 (tt0) cc_final: 0.7534 (tt0) REVERT: A 505 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8446 (tp) REVERT: B 47 SER cc_start: 0.8392 (t) cc_final: 0.8189 (t) REVERT: B 50 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7614 (mmtm) REVERT: B 194 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.8146 (tpp80) REVERT: B 272 ARG cc_start: 0.8110 (tpp-160) cc_final: 0.7622 (ttp80) REVERT: B 323 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6797 (tpt170) REVERT: B 405 MET cc_start: 0.7252 (mtp) cc_final: 0.6412 (mtp) REVERT: B 409 TRP cc_start: 0.8683 (OUTLIER) cc_final: 0.7318 (m-90) REVERT: B 420 GLN cc_start: 0.7967 (tt0) cc_final: 0.7730 (tt0) REVERT: B 453 ILE cc_start: 0.8127 (mm) cc_final: 0.7754 (mm) REVERT: B 456 PHE cc_start: 0.7847 (t80) cc_final: 0.7475 (t80) REVERT: B 471 TRP cc_start: 0.8647 (m100) cc_final: 0.8445 (m100) REVERT: B 532 ASN cc_start: 0.8674 (m-40) cc_final: 0.8402 (m-40) REVERT: B 619 MET cc_start: 0.9062 (ttm) cc_final: 0.8738 (ttp) REVERT: B 710 MET cc_start: 0.9098 (tpp) cc_final: 0.8889 (tpp) REVERT: B 721 MET cc_start: 0.8835 (mmt) cc_final: 0.8560 (mmp) REVERT: B 737 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7517 (mmmt) REVERT: C 194 ARG cc_start: 0.8415 (tpp80) cc_final: 0.8149 (tpp-160) REVERT: C 272 ARG cc_start: 0.7089 (ttp80) cc_final: 0.6599 (ttp80) REVERT: C 339 LEU cc_start: 0.8753 (mt) cc_final: 0.8550 (mp) REVERT: C 403 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5713 (tp30) REVERT: C 405 MET cc_start: 0.7398 (mtp) cc_final: 0.6696 (mtp) REVERT: C 409 TRP cc_start: 0.8667 (OUTLIER) cc_final: 0.7479 (m-90) REVERT: C 419 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8019 (ttmt) REVERT: C 505 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8614 (tp) REVERT: C 532 ASN cc_start: 0.8630 (m-40) cc_final: 0.8363 (m-40) REVERT: C 619 MET cc_start: 0.9006 (ttp) cc_final: 0.8545 (ttp) REVERT: C 737 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7666 (mmmm) REVERT: C 740 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8042 (mttp) REVERT: D 272 ARG cc_start: 0.7169 (ttp80) cc_final: 0.6756 (ttp80) REVERT: D 294 LYS cc_start: 0.8851 (tttm) cc_final: 0.8431 (tmtt) REVERT: D 405 MET cc_start: 0.7257 (mtp) cc_final: 0.6570 (mtp) REVERT: D 409 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.7201 (m-90) REVERT: D 532 ASN cc_start: 0.8887 (m-40) cc_final: 0.8315 (m-40) REVERT: D 536 GLN cc_start: 0.9177 (tp40) cc_final: 0.8415 (tp40) REVERT: D 583 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9036 (t) REVERT: D 619 MET cc_start: 0.9022 (ttm) cc_final: 0.8626 (ttp) REVERT: D 648 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7767 (pt0) REVERT: D 737 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7542 (mmmm) outliers start: 86 outliers final: 43 residues processed: 486 average time/residue: 0.1575 time to fit residues: 120.2894 Evaluate side-chains 434 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 381 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 549 CYS Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 741 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 99 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 126 optimal weight: 0.0270 chunk 88 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 0.0000 overall best weight: 0.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 741 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.139927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.109373 restraints weight = 28328.318| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.03 r_work: 0.3029 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21906 Z= 0.123 Angle : 0.533 9.957 29714 Z= 0.276 Chirality : 0.041 0.382 3393 Planarity : 0.004 0.053 3668 Dihedral : 10.249 116.783 3103 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.17 % Allowed : 15.08 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2601 helix: 0.97 (0.12), residues: 1877 sheet: None (None), residues: 0 loop : -2.35 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 296 TYR 0.020 0.001 TYR A 523 PHE 0.023 0.001 PHE C 340 TRP 0.012 0.001 TRP C 635 HIS 0.001 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (21899) covalent geometry : angle 0.53163 / 0.28 (29706) SS BOND : bond 0.01087 / 0.52 ( 4) SS BOND : angle 2.09929 / 1.42 ( 8) hydrogen bonds : bond 0.03799 / 2.52 ( 1277) hydrogen bonds : angle 3.66102 / 2.61 ( 3720) Misc. bond : bond 0.00082 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 431 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8251 (pt) REVERT: A 215 ASP cc_start: 0.8314 (p0) cc_final: 0.7811 (p0) REVERT: A 323 ARG cc_start: 0.7438 (mtt180) cc_final: 0.7175 (tpt170) REVERT: A 419 LYS cc_start: 0.8621 (tptm) cc_final: 0.8416 (ttmt) REVERT: A 420 GLN cc_start: 0.7896 (tt0) cc_final: 0.7450 (tt0) REVERT: A 505 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8399 (tp) REVERT: A 558 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 634 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8484 (tp30) REVERT: B 50 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7816 (mmtp) REVERT: B 79 GLU cc_start: 0.8299 (tt0) cc_final: 0.7974 (mt-10) REVERT: B 194 ARG cc_start: 0.8427 (tpp-160) cc_final: 0.8189 (tpp80) REVERT: B 243 GLU cc_start: 0.8415 (tt0) cc_final: 0.8054 (pt0) REVERT: B 272 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7443 (ttp80) REVERT: B 323 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6870 (tpt170) REVERT: B 340 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8062 (p90) REVERT: B 405 MET cc_start: 0.7228 (mtp) cc_final: 0.6313 (mtp) REVERT: B 409 TRP cc_start: 0.8693 (OUTLIER) cc_final: 0.7384 (m-90) REVERT: B 420 GLN cc_start: 0.7979 (tt0) cc_final: 0.7720 (tt0) REVERT: B 453 ILE cc_start: 0.8153 (mm) cc_final: 0.7798 (mm) REVERT: B 456 PHE cc_start: 0.7728 (t80) cc_final: 0.7347 (t80) REVERT: B 471 TRP cc_start: 0.8554 (m100) cc_final: 0.8331 (m100) REVERT: B 532 ASN cc_start: 0.8598 (m-40) cc_final: 0.8254 (m-40) REVERT: B 583 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9036 (t) REVERT: B 619 MET cc_start: 0.9054 (ttm) cc_final: 0.8717 (ttp) REVERT: B 737 LYS cc_start: 0.8027 (mmtm) cc_final: 0.7497 (mmmt) REVERT: C 194 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8023 (tpp-160) REVERT: C 272 ARG cc_start: 0.7075 (ttp80) cc_final: 0.6540 (ttp80) REVERT: C 403 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5788 (tp30) REVERT: C 405 MET cc_start: 0.7375 (mtp) cc_final: 0.6568 (mtp) REVERT: C 409 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7360 (m-90) REVERT: C 419 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8030 (ttmt) REVERT: C 456 PHE cc_start: 0.7941 (t80) cc_final: 0.7393 (t80) REVERT: C 505 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 532 ASN cc_start: 0.8627 (m-40) cc_final: 0.8405 (t0) REVERT: C 583 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9106 (t) REVERT: C 737 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7644 (mmmm) REVERT: D 215 ASP cc_start: 0.8226 (p0) cc_final: 0.7804 (p0) REVERT: D 272 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6787 (ttp80) REVERT: D 294 LYS cc_start: 0.8853 (tttm) cc_final: 0.8457 (tmtt) REVERT: D 409 TRP cc_start: 0.8464 (OUTLIER) cc_final: 0.7186 (m-90) REVERT: D 420 GLN cc_start: 0.8093 (tt0) cc_final: 0.7825 (tt0) REVERT: D 456 PHE cc_start: 0.7822 (t80) cc_final: 0.7416 (t80) REVERT: D 583 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9056 (t) REVERT: D 619 MET cc_start: 0.8976 (ttm) cc_final: 0.8632 (ttp) REVERT: D 737 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7537 (mmmm) outliers start: 92 outliers final: 36 residues processed: 491 average time/residue: 0.1535 time to fit residues: 119.4954 Evaluate side-chains 447 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 397 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 97 optimal weight: 0.5980 chunk 257 optimal weight: 0.0170 chunk 186 optimal weight: 0.7980 chunk 250 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 205 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 506 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C 442 ASN C 506 GLN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 506 GLN D 741 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.145015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115983 restraints weight = 27926.237| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.94 r_work: 0.3085 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21906 Z= 0.128 Angle : 0.532 10.112 29714 Z= 0.274 Chirality : 0.042 0.374 3393 Planarity : 0.004 0.052 3668 Dihedral : 10.036 116.520 3101 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.08 % Allowed : 15.72 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2601 helix: 1.23 (0.12), residues: 1893 sheet: None (None), residues: 0 loop : -2.26 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 296 TYR 0.020 0.001 TYR C 523 PHE 0.026 0.002 PHE C 340 TRP 0.011 0.001 TRP C 635 HIS 0.002 0.000 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21899) covalent geometry : angle 0.53106 / 0.27 (29706) SS BOND : bond 0.00311 / 0.15 ( 4) SS BOND : angle 2.00683 / 1.32 ( 8) hydrogen bonds : bond 0.03751 / 2.50 ( 1277) hydrogen bonds : angle 3.54904 / 2.52 ( 3720) Misc. bond : bond 0.00184 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 427 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8262 (pt) REVERT: A 113 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 215 ASP cc_start: 0.8211 (p0) cc_final: 0.7758 (p0) REVERT: A 323 ARG cc_start: 0.7500 (mtt180) cc_final: 0.7213 (tpt170) REVERT: A 419 LYS cc_start: 0.8611 (tptm) cc_final: 0.8409 (ttmt) REVERT: A 420 GLN cc_start: 0.7914 (tt0) cc_final: 0.7503 (tt0) REVERT: A 470 MET cc_start: 0.7777 (tmm) cc_final: 0.7456 (tmm) REVERT: A 505 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8428 (tp) REVERT: A 538 TYR cc_start: 0.8800 (m-80) cc_final: 0.8483 (m-80) REVERT: A 558 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8042 (p0) REVERT: B 50 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7024 (mmtp) REVERT: B 54 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 79 GLU cc_start: 0.8257 (tt0) cc_final: 0.7827 (mm-30) REVERT: B 194 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8211 (tpp80) REVERT: B 243 GLU cc_start: 0.8404 (tt0) cc_final: 0.8089 (pt0) REVERT: B 272 ARG cc_start: 0.7927 (tpp-160) cc_final: 0.7506 (ttp80) REVERT: B 340 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8117 (p90) REVERT: B 405 MET cc_start: 0.7555 (mtp) cc_final: 0.6736 (mtp) REVERT: B 409 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.7393 (m-90) REVERT: B 420 GLN cc_start: 0.8010 (tt0) cc_final: 0.7713 (tt0) REVERT: B 453 ILE cc_start: 0.8159 (mm) cc_final: 0.7800 (mm) REVERT: B 532 ASN cc_start: 0.8624 (m-40) cc_final: 0.8414 (t0) REVERT: B 535 ASN cc_start: 0.9331 (t0) cc_final: 0.9122 (t0) REVERT: B 583 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9049 (t) REVERT: B 737 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7536 (mmmm) REVERT: C 38 ASN cc_start: 0.8628 (t0) cc_final: 0.7974 (t0) REVERT: C 42 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8214 (mtmt) REVERT: C 79 GLU cc_start: 0.8212 (tt0) cc_final: 0.7898 (tt0) REVERT: C 194 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8109 (tpp-160) REVERT: C 272 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6791 (ttp80) REVERT: C 403 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6151 (tp30) REVERT: C 405 MET cc_start: 0.7431 (mtp) cc_final: 0.6686 (mtp) REVERT: C 409 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.7408 (m-90) REVERT: C 505 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8531 (tp) REVERT: C 536 GLN cc_start: 0.8812 (tp40) cc_final: 0.8599 (tp40) REVERT: C 583 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9141 (t) REVERT: C 737 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7613 (mmmm) REVERT: D 113 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7826 (mt-10) REVERT: D 215 ASP cc_start: 0.8238 (p0) cc_final: 0.7766 (p0) REVERT: D 272 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7003 (ttp80) REVERT: D 294 LYS cc_start: 0.8971 (tttm) cc_final: 0.8567 (tmtt) REVERT: D 405 MET cc_start: 0.7517 (mtp) cc_final: 0.6734 (mtp) REVERT: D 409 TRP cc_start: 0.8515 (OUTLIER) cc_final: 0.7254 (m-90) REVERT: D 419 LYS cc_start: 0.8486 (tptm) cc_final: 0.8267 (ttmt) REVERT: D 456 PHE cc_start: 0.7779 (t80) cc_final: 0.7363 (t80) REVERT: D 536 GLN cc_start: 0.9204 (tp40) cc_final: 0.8464 (tp40) REVERT: D 583 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9051 (t) REVERT: D 619 MET cc_start: 0.8904 (ttm) cc_final: 0.8561 (ttp) REVERT: D 737 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7606 (mmmm) REVERT: D 748 PHE cc_start: 0.8758 (m-80) cc_final: 0.8537 (m-10) outliers start: 90 outliers final: 43 residues processed: 483 average time/residue: 0.1490 time to fit residues: 114.7596 Evaluate side-chains 462 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 18 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 187 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 442 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN D 442 ASN D 741 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.105319 restraints weight = 28289.996| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.06 r_work: 0.2953 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21906 Z= 0.147 Angle : 0.551 10.988 29714 Z= 0.284 Chirality : 0.042 0.355 3393 Planarity : 0.004 0.051 3668 Dihedral : 9.847 116.196 3095 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.99 % Allowed : 16.08 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2601 helix: 1.42 (0.12), residues: 1882 sheet: None (None), residues: 0 loop : -2.14 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 296 TYR 0.022 0.001 TYR C 523 PHE 0.027 0.002 PHE B 456 TRP 0.028 0.001 TRP A 409 HIS 0.002 0.001 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21899) covalent geometry : angle 0.54815 / 0.28 (29706) SS BOND : bond 0.00747 / 0.36 ( 4) SS BOND : angle 3.33353 / 1.87 ( 8) hydrogen bonds : bond 0.03858 / 2.55 ( 1277) hydrogen bonds : angle 3.53883 / 2.51 ( 3720) Misc. bond : bond 0.00305 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 417 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8313 (pt) REVERT: A 215 ASP cc_start: 0.8198 (p0) cc_final: 0.7744 (p0) REVERT: A 323 ARG cc_start: 0.7526 (mtt180) cc_final: 0.7272 (tpt170) REVERT: A 405 MET cc_start: 0.7552 (mtp) cc_final: 0.7201 (mtm) REVERT: A 419 LYS cc_start: 0.8632 (tptm) cc_final: 0.8400 (ttmt) REVERT: A 420 GLN cc_start: 0.7838 (tt0) cc_final: 0.7434 (tt0) REVERT: A 505 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8471 (tp) REVERT: A 558 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8208 (p0) REVERT: B 50 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7014 (mmtp) REVERT: B 54 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 79 GLU cc_start: 0.8312 (tt0) cc_final: 0.7900 (mm-30) REVERT: B 194 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.8288 (tpp80) REVERT: B 243 GLU cc_start: 0.8416 (tt0) cc_final: 0.8045 (pt0) REVERT: B 272 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7471 (ttp80) REVERT: B 340 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8009 (p90) REVERT: B 401 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7089 (tp) REVERT: B 405 MET cc_start: 0.7818 (mtp) cc_final: 0.6859 (mtp) REVERT: B 409 TRP cc_start: 0.8742 (OUTLIER) cc_final: 0.7374 (m-90) REVERT: B 420 GLN cc_start: 0.8035 (tt0) cc_final: 0.7791 (tt0) REVERT: B 456 PHE cc_start: 0.7939 (t80) cc_final: 0.7606 (t80) REVERT: B 532 ASN cc_start: 0.8571 (m-40) cc_final: 0.8329 (t0) REVERT: B 535 ASN cc_start: 0.9367 (t0) cc_final: 0.9158 (t0) REVERT: B 583 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9083 (t) REVERT: B 721 MET cc_start: 0.8819 (mmt) cc_final: 0.8578 (mmp) REVERT: B 737 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7475 (mmmm) REVERT: C 38 ASN cc_start: 0.8656 (t0) cc_final: 0.8411 (t0) REVERT: C 42 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8332 (mtpp) REVERT: C 79 GLU cc_start: 0.8281 (tt0) cc_final: 0.8041 (tt0) REVERT: C 113 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 194 ARG cc_start: 0.8521 (tpp80) cc_final: 0.8169 (tpp-160) REVERT: C 215 ASP cc_start: 0.8449 (p0) cc_final: 0.7910 (p0) REVERT: C 272 ARG cc_start: 0.7362 (ttp80) cc_final: 0.6867 (ttp80) REVERT: C 405 MET cc_start: 0.7589 (mtp) cc_final: 0.6778 (mtp) REVERT: C 409 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.7449 (m-90) REVERT: C 470 MET cc_start: 0.7695 (tmm) cc_final: 0.7398 (tmm) REVERT: C 536 GLN cc_start: 0.8938 (tp40) cc_final: 0.8525 (tp40) REVERT: C 583 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9118 (t) REVERT: C 737 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7559 (mmmm) REVERT: D 79 GLU cc_start: 0.8378 (tt0) cc_final: 0.8130 (tt0) REVERT: D 215 ASP cc_start: 0.8357 (p0) cc_final: 0.7877 (p0) REVERT: D 272 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7139 (ttp80) REVERT: D 294 LYS cc_start: 0.8959 (tttm) cc_final: 0.8552 (tmtt) REVERT: D 405 MET cc_start: 0.7728 (mtp) cc_final: 0.6472 (mtm) REVERT: D 409 TRP cc_start: 0.8613 (OUTLIER) cc_final: 0.7309 (m-90) REVERT: D 419 LYS cc_start: 0.8511 (tptm) cc_final: 0.8234 (ttmt) REVERT: D 453 ILE cc_start: 0.8156 (mm) cc_final: 0.7936 (mm) REVERT: D 619 MET cc_start: 0.8937 (ttm) cc_final: 0.8602 (ttp) REVERT: D 737 LYS cc_start: 0.8049 (mmtm) cc_final: 0.7624 (mmmm) outliers start: 88 outliers final: 52 residues processed: 479 average time/residue: 0.1521 time to fit residues: 115.3352 Evaluate side-chains 470 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 406 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 741 GLN Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 106 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 180 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 442 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN D 442 ASN D 741 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115251 restraints weight = 27994.821| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.95 r_work: 0.2983 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21906 Z= 0.126 Angle : 0.532 10.828 29714 Z= 0.273 Chirality : 0.041 0.415 3393 Planarity : 0.004 0.049 3668 Dihedral : 9.623 116.453 3093 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.40 % Allowed : 16.89 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2601 helix: 1.54 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -2.09 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 296 TYR 0.020 0.001 TYR C 523 PHE 0.027 0.002 PHE D 340 TRP 0.022 0.001 TRP A 409 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21899) covalent geometry : angle 0.52956 / 0.27 (29706) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 3.11388 / 1.71 ( 8) hydrogen bonds : bond 0.03670 / 2.43 ( 1277) hydrogen bonds : angle 3.47908 / 2.46 ( 3720) Misc. bond : bond 0.00282 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 423 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8314 (pt) REVERT: A 215 ASP cc_start: 0.8093 (p0) cc_final: 0.7843 (p0) REVERT: A 323 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7249 (tpt170) REVERT: A 405 MET cc_start: 0.7628 (mtp) cc_final: 0.7138 (mtm) REVERT: A 419 LYS cc_start: 0.8653 (tptm) cc_final: 0.8426 (ttmt) REVERT: A 420 GLN cc_start: 0.7725 (tt0) cc_final: 0.7401 (tt0) REVERT: A 505 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8433 (tp) REVERT: A 556 LYS cc_start: 0.8149 (tptt) cc_final: 0.7916 (tptt) REVERT: A 558 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8161 (p0) REVERT: B 50 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7026 (mmtp) REVERT: B 54 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: B 79 GLU cc_start: 0.8311 (tt0) cc_final: 0.7906 (mm-30) REVERT: B 194 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8273 (tpp80) REVERT: B 215 ASP cc_start: 0.8101 (p0) cc_final: 0.7799 (p0) REVERT: B 243 GLU cc_start: 0.8372 (tt0) cc_final: 0.8035 (pt0) REVERT: B 272 ARG cc_start: 0.7837 (tpp-160) cc_final: 0.7475 (ttp80) REVERT: B 340 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8064 (p90) REVERT: B 401 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7142 (tp) REVERT: B 405 MET cc_start: 0.7779 (mtp) cc_final: 0.6840 (mtp) REVERT: B 409 TRP cc_start: 0.8712 (OUTLIER) cc_final: 0.7391 (m-90) REVERT: B 420 GLN cc_start: 0.8052 (tt0) cc_final: 0.7794 (tt0) REVERT: B 456 PHE cc_start: 0.7768 (t80) cc_final: 0.7551 (t80) REVERT: B 532 ASN cc_start: 0.8554 (m-40) cc_final: 0.8336 (t0) REVERT: B 535 ASN cc_start: 0.9338 (t0) cc_final: 0.9117 (t0) REVERT: B 556 LYS cc_start: 0.8255 (tptt) cc_final: 0.8038 (tptt) REVERT: B 583 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9087 (t) REVERT: B 634 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: B 737 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7470 (mmmm) REVERT: C 38 ASN cc_start: 0.8670 (t0) cc_final: 0.7964 (t0) REVERT: C 42 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8045 (mtmt) REVERT: C 79 GLU cc_start: 0.8272 (tt0) cc_final: 0.8016 (tt0) REVERT: C 194 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8181 (tpp-160) REVERT: C 215 ASP cc_start: 0.8409 (p0) cc_final: 0.7877 (p0) REVERT: C 272 ARG cc_start: 0.7359 (ttp80) cc_final: 0.6868 (ttp80) REVERT: C 405 MET cc_start: 0.7713 (mtp) cc_final: 0.6817 (mtp) REVERT: C 409 TRP cc_start: 0.8675 (OUTLIER) cc_final: 0.7390 (m-90) REVERT: C 470 MET cc_start: 0.7635 (tmm) cc_final: 0.7370 (tmm) REVERT: C 536 GLN cc_start: 0.8921 (tp40) cc_final: 0.8667 (tp40) REVERT: C 583 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9131 (t) REVERT: C 737 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7620 (mmmm) REVERT: D 113 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 215 ASP cc_start: 0.8252 (p0) cc_final: 0.7791 (p0) REVERT: D 272 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7152 (ttp80) REVERT: D 294 LYS cc_start: 0.8943 (tttm) cc_final: 0.8543 (tmtt) REVERT: D 405 MET cc_start: 0.7747 (mtp) cc_final: 0.6375 (mtm) REVERT: D 409 TRP cc_start: 0.8559 (OUTLIER) cc_final: 0.7150 (m-90) REVERT: D 453 ILE cc_start: 0.8179 (mm) cc_final: 0.7977 (mm) REVERT: D 536 GLN cc_start: 0.9195 (tp40) cc_final: 0.8386 (tp40) REVERT: D 583 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9091 (t) REVERT: D 737 LYS cc_start: 0.8059 (mmtm) cc_final: 0.7667 (mmmm) outliers start: 75 outliers final: 48 residues processed: 475 average time/residue: 0.1479 time to fit residues: 111.3112 Evaluate side-chains 467 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 405 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 442 ASN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 741 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 215 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 203 optimal weight: 4.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 442 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 703 HIS D 741 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113405 restraints weight = 27997.944| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.92 r_work: 0.3071 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21906 Z= 0.141 Angle : 0.548 10.654 29714 Z= 0.281 Chirality : 0.042 0.413 3393 Planarity : 0.004 0.049 3668 Dihedral : 9.543 116.180 3093 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.58 % Allowed : 16.80 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2601 helix: 1.61 (0.12), residues: 1880 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 296 TYR 0.021 0.001 TYR C 523 PHE 0.028 0.002 PHE A 378 TRP 0.018 0.001 TRP A 409 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (21899) covalent geometry : angle 0.54617 / 0.28 (29706) SS BOND : bond 0.00408 / 0.21 ( 4) SS BOND : angle 2.87784 / 1.66 ( 8) hydrogen bonds : bond 0.03731 / 2.47 ( 1277) hydrogen bonds : angle 3.49763 / 2.47 ( 3720) Misc. bond : bond 0.00308 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 414 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8284 (pt) REVERT: A 215 ASP cc_start: 0.8066 (p0) cc_final: 0.7816 (p0) REVERT: A 405 MET cc_start: 0.7700 (mtp) cc_final: 0.7161 (mtm) REVERT: A 419 LYS cc_start: 0.8689 (tptm) cc_final: 0.8449 (ttmt) REVERT: A 420 GLN cc_start: 0.7776 (tt0) cc_final: 0.7453 (tt0) REVERT: A 505 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8540 (tp) REVERT: A 535 ASN cc_start: 0.9335 (t0) cc_final: 0.9117 (t0) REVERT: A 536 GLN cc_start: 0.9252 (tp40) cc_final: 0.8870 (tp40) REVERT: A 558 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (p0) REVERT: B 50 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7090 (mmtp) REVERT: B 54 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: B 79 GLU cc_start: 0.8322 (tt0) cc_final: 0.7893 (mm-30) REVERT: B 194 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8319 (tpp80) REVERT: B 215 ASP cc_start: 0.8149 (p0) cc_final: 0.7850 (p0) REVERT: B 243 GLU cc_start: 0.8425 (tt0) cc_final: 0.8089 (pt0) REVERT: B 272 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7529 (ttp80) REVERT: B 340 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8045 (p90) REVERT: B 401 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7241 (tp) REVERT: B 405 MET cc_start: 0.7830 (mtp) cc_final: 0.6899 (mtp) REVERT: B 409 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.7403 (m-90) REVERT: B 420 GLN cc_start: 0.8101 (tt0) cc_final: 0.7824 (tt0) REVERT: B 456 PHE cc_start: 0.7764 (t80) cc_final: 0.7544 (t80) REVERT: B 532 ASN cc_start: 0.8618 (m-40) cc_final: 0.8390 (t0) REVERT: B 535 ASN cc_start: 0.9345 (t0) cc_final: 0.9136 (t0) REVERT: B 583 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9078 (t) REVERT: B 634 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: B 721 MET cc_start: 0.8745 (mmt) cc_final: 0.8457 (mmp) REVERT: B 737 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7596 (mmmm) REVERT: C 38 ASN cc_start: 0.8676 (t0) cc_final: 0.7949 (t0) REVERT: C 42 LYS cc_start: 0.8546 (mtpp) cc_final: 0.7993 (mtmt) REVERT: C 79 GLU cc_start: 0.8278 (tt0) cc_final: 0.8024 (tt0) REVERT: C 194 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8212 (tpp-160) REVERT: C 215 ASP cc_start: 0.8410 (p0) cc_final: 0.7897 (p0) REVERT: C 272 ARG cc_start: 0.7425 (ttp80) cc_final: 0.6956 (ttp80) REVERT: C 405 MET cc_start: 0.7760 (mtp) cc_final: 0.6809 (mtp) REVERT: C 409 TRP cc_start: 0.8681 (OUTLIER) cc_final: 0.7421 (m-90) REVERT: C 453 ILE cc_start: 0.8129 (mm) cc_final: 0.7871 (mm) REVERT: C 470 MET cc_start: 0.7684 (tmm) cc_final: 0.7457 (tmm) REVERT: C 536 GLN cc_start: 0.8921 (tp40) cc_final: 0.8498 (tp40) REVERT: C 583 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9159 (t) REVERT: C 737 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7975 (mmmm) REVERT: D 15 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6587 (ttt-90) REVERT: D 215 ASP cc_start: 0.8256 (p0) cc_final: 0.7808 (p0) REVERT: D 272 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7187 (ttp80) REVERT: D 294 LYS cc_start: 0.8947 (tttm) cc_final: 0.8578 (tmtt) REVERT: D 404 TRP cc_start: 0.8183 (m100) cc_final: 0.7939 (m100) REVERT: D 405 MET cc_start: 0.7821 (mtp) cc_final: 0.6361 (mtm) REVERT: D 409 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.7106 (m-90) REVERT: D 419 LYS cc_start: 0.8559 (tptm) cc_final: 0.8261 (ttmt) REVERT: D 453 ILE cc_start: 0.8192 (mm) cc_final: 0.7982 (mm) REVERT: D 536 GLN cc_start: 0.9187 (tp40) cc_final: 0.8519 (tp40) REVERT: D 737 LYS cc_start: 0.8085 (mmtm) cc_final: 0.7716 (mmmm) outliers start: 79 outliers final: 54 residues processed: 474 average time/residue: 0.1520 time to fit residues: 114.4147 Evaluate side-chains 463 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 396 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 741 GLN Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 256 optimal weight: 0.6980 chunk 180 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN A 435 ASN A 442 ASN ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115861 restraints weight = 27747.750| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.94 r_work: 0.3017 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21906 Z= 0.124 Angle : 0.538 10.227 29714 Z= 0.277 Chirality : 0.041 0.412 3393 Planarity : 0.004 0.050 3668 Dihedral : 9.417 116.367 3093 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 2.94 % Allowed : 17.44 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2601 helix: 1.65 (0.12), residues: 1887 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 296 TYR 0.020 0.001 TYR C 523 PHE 0.028 0.002 PHE D 456 TRP 0.017 0.001 TRP D 468 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (21899) covalent geometry : angle 0.53687 / 0.28 (29706) SS BOND : bond 0.00153 / 0.08 ( 4) SS BOND : angle 2.36775 / 1.38 ( 8) hydrogen bonds : bond 0.03605 / 2.38 ( 1277) hydrogen bonds : angle 3.48440 / 2.45 ( 3720) Misc. bond : bond 0.00308 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 430 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8300 (pt) REVERT: A 215 ASP cc_start: 0.7990 (p0) cc_final: 0.7700 (p0) REVERT: A 405 MET cc_start: 0.7669 (mtp) cc_final: 0.7111 (mtm) REVERT: A 470 MET cc_start: 0.7959 (tmm) cc_final: 0.7580 (tmm) REVERT: A 505 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 558 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8283 (p0) REVERT: A 733 GLU cc_start: 0.8248 (tt0) cc_final: 0.7908 (tt0) REVERT: B 50 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7070 (mmtm) REVERT: B 54 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 79 GLU cc_start: 0.8342 (tt0) cc_final: 0.7930 (mm-30) REVERT: B 194 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8288 (tpp80) REVERT: B 215 ASP cc_start: 0.8049 (p0) cc_final: 0.7735 (p0) REVERT: B 243 GLU cc_start: 0.8383 (tt0) cc_final: 0.8050 (pt0) REVERT: B 272 ARG cc_start: 0.7888 (tpp-160) cc_final: 0.7529 (ttp80) REVERT: B 340 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8019 (p90) REVERT: B 401 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7325 (tp) REVERT: B 405 MET cc_start: 0.7837 (mtp) cc_final: 0.6822 (mtp) REVERT: B 409 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.7316 (m-90) REVERT: B 420 GLN cc_start: 0.8076 (tt0) cc_final: 0.7835 (tt0) REVERT: B 456 PHE cc_start: 0.7770 (t80) cc_final: 0.7541 (t80) REVERT: B 470 MET cc_start: 0.7518 (tmm) cc_final: 0.7317 (tmm) REVERT: B 532 ASN cc_start: 0.8597 (m-40) cc_final: 0.8361 (t0) REVERT: B 535 ASN cc_start: 0.9350 (t0) cc_final: 0.9113 (t0) REVERT: B 583 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9073 (t) REVERT: B 634 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: B 737 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7557 (mmmm) REVERT: C 79 GLU cc_start: 0.8278 (tt0) cc_final: 0.8002 (tt0) REVERT: C 113 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7470 (pt0) REVERT: C 194 ARG cc_start: 0.8541 (tpp80) cc_final: 0.8213 (tpp-160) REVERT: C 215 ASP cc_start: 0.8391 (p0) cc_final: 0.7877 (p0) REVERT: C 272 ARG cc_start: 0.7390 (ttp80) cc_final: 0.6922 (ttp80) REVERT: C 405 MET cc_start: 0.7733 (mtp) cc_final: 0.6718 (mtp) REVERT: C 409 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.7340 (m-90) REVERT: C 453 ILE cc_start: 0.8088 (mm) cc_final: 0.7827 (mm) REVERT: C 470 MET cc_start: 0.7730 (tmm) cc_final: 0.7523 (tmm) REVERT: C 536 GLN cc_start: 0.9010 (tp40) cc_final: 0.8772 (tp40) REVERT: C 583 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9119 (t) REVERT: C 737 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7947 (mmmm) REVERT: D 15 ARG cc_start: 0.7175 (ttp-110) cc_final: 0.6558 (ttt-90) REVERT: D 194 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8256 (tpp-160) REVERT: D 272 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7129 (ttp80) REVERT: D 294 LYS cc_start: 0.8946 (tttm) cc_final: 0.8568 (tmtt) REVERT: D 404 TRP cc_start: 0.8194 (m100) cc_final: 0.7950 (m100) REVERT: D 405 MET cc_start: 0.7842 (mtp) cc_final: 0.6421 (mtm) REVERT: D 409 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7187 (m-90) REVERT: D 420 GLN cc_start: 0.8039 (tt0) cc_final: 0.7755 (tt0) REVERT: D 536 GLN cc_start: 0.9190 (tp40) cc_final: 0.8559 (tp40) REVERT: D 583 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9063 (t) REVERT: D 737 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7762 (mmmm) outliers start: 65 outliers final: 46 residues processed: 479 average time/residue: 0.1494 time to fit residues: 113.3427 Evaluate side-chains 467 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 407 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 576 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 741 GLN Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 435 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.133428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102463 restraints weight = 28302.790| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.03 r_work: 0.2896 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21906 Z= 0.198 Angle : 0.616 13.195 29714 Z= 0.316 Chirality : 0.044 0.348 3393 Planarity : 0.004 0.050 3668 Dihedral : 9.590 115.905 3093 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 2.99 % Allowed : 17.89 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2601 helix: 1.50 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : -1.99 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 296 TYR 0.026 0.002 TYR C 523 PHE 0.029 0.002 PHE D 340 TRP 0.021 0.001 TRP D 468 HIS 0.003 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (21899) covalent geometry : angle 0.61430 / 0.32 (29706) SS BOND : bond 0.00209 / 0.11 ( 4) SS BOND : angle 2.72197 / 1.70 ( 8) hydrogen bonds : bond 0.04149 / 2.75 ( 1277) hydrogen bonds : angle 3.68740 / 2.58 ( 3720) Misc. bond : bond 0.00291 / 0.15 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 413 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8047 (mtpp) REVERT: A 63 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8448 (pt) REVERT: A 194 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.8141 (tpp80) REVERT: A 215 ASP cc_start: 0.8260 (p0) cc_final: 0.7949 (p0) REVERT: A 405 MET cc_start: 0.7892 (mtp) cc_final: 0.7312 (mtm) REVERT: A 470 MET cc_start: 0.8018 (tmm) cc_final: 0.7628 (tmm) REVERT: A 505 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 536 GLN cc_start: 0.9295 (tp40) cc_final: 0.9086 (tp40) REVERT: A 558 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (p0) REVERT: B 50 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7964 (mmtm) REVERT: B 194 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8327 (tpp80) REVERT: B 215 ASP cc_start: 0.8283 (p0) cc_final: 0.7932 (p0) REVERT: B 272 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7477 (ttp80) REVERT: B 294 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8681 (tptt) REVERT: B 340 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8003 (p90) REVERT: B 401 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7303 (tp) REVERT: B 405 MET cc_start: 0.8049 (mtp) cc_final: 0.7112 (mtp) REVERT: B 409 TRP cc_start: 0.8757 (OUTLIER) cc_final: 0.7421 (m-90) REVERT: B 420 GLN cc_start: 0.8030 (tt0) cc_final: 0.7721 (tt0) REVERT: B 453 ILE cc_start: 0.8140 (mm) cc_final: 0.7882 (mm) REVERT: B 470 MET cc_start: 0.7579 (tmm) cc_final: 0.7375 (tmm) REVERT: B 532 ASN cc_start: 0.8608 (m-40) cc_final: 0.8360 (t0) REVERT: B 535 ASN cc_start: 0.9404 (t0) cc_final: 0.9198 (t0) REVERT: B 621 ASN cc_start: 0.8624 (m-40) cc_final: 0.8109 (m-40) REVERT: B 634 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8320 (mt-10) REVERT: B 721 MET cc_start: 0.8843 (mmt) cc_final: 0.8572 (mmt) REVERT: B 737 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7747 (mmmm) REVERT: C 42 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8377 (mtpp) REVERT: C 79 GLU cc_start: 0.8376 (tt0) cc_final: 0.8050 (tt0) REVERT: C 113 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 194 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8254 (tpp-160) REVERT: C 272 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6892 (ttp80) REVERT: C 294 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8673 (tptt) REVERT: C 405 MET cc_start: 0.8067 (mtp) cc_final: 0.7104 (mtp) REVERT: C 409 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.7419 (m-90) REVERT: C 420 GLN cc_start: 0.8134 (tt0) cc_final: 0.7759 (tt0) REVERT: C 470 MET cc_start: 0.7765 (tmm) cc_final: 0.7521 (tmm) REVERT: C 558 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8306 (p0) REVERT: C 737 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7910 (mmmm) REVERT: D 194 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8380 (tpp-160) REVERT: D 272 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7151 (ttp80) REVERT: D 294 LYS cc_start: 0.8906 (tttm) cc_final: 0.8509 (tmtt) REVERT: D 405 MET cc_start: 0.7928 (mtp) cc_final: 0.6490 (mtm) REVERT: D 409 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.7369 (m-90) REVERT: D 419 LYS cc_start: 0.8486 (tptm) cc_final: 0.8053 (ttmt) REVERT: D 737 LYS cc_start: 0.8327 (mmtm) cc_final: 0.7965 (mmmm) outliers start: 66 outliers final: 51 residues processed: 466 average time/residue: 0.1480 time to fit residues: 107.9502 Evaluate side-chains 454 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 392 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 576 PHE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 558 ASN Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 576 PHE Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 576 PHE Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 741 GLN Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 75 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 741 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103533 restraints weight = 28366.715| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.01 r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21906 Z= 0.166 Angle : 0.594 13.271 29714 Z= 0.306 Chirality : 0.043 0.303 3393 Planarity : 0.004 0.051 3668 Dihedral : 9.594 115.994 3093 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 2.94 % Allowed : 18.70 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.17), residues: 2601 helix: 1.49 (0.12), residues: 1886 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 296 TYR 0.024 0.001 TYR C 523 PHE 0.027 0.002 PHE D 340 TRP 0.019 0.001 TRP D 468 HIS 0.002 0.001 HIS C 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (21899) covalent geometry : angle 0.59295 / 0.31 (29706) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 2.57218 / 1.59 ( 8) hydrogen bonds : bond 0.03942 / 2.61 ( 1277) hydrogen bonds : angle 3.66867 / 2.57 ( 3720) Misc. bond : bond 0.00320 / 0.17 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5814.25 seconds wall clock time: 100 minutes 25.50 seconds (6025.50 seconds total)