Starting phenix.real_space_refine on Fri Jun 5 14:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jzo_9898/06_2026/6jzo_9898.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jzo_9898/06_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_9898/06_2026/6jzo_9898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jzo_9898/06_2026/6jzo_9898.map" model { file = "/net/cci-nas-00/data/ceres_data/6jzo_9898/06_2026/6jzo_9898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jzo_9898/06_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/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: 5.09, 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: 1.46 Conformation dependent library (CDL) restraints added in 911.6 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: 0.62 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: 3.29 Time building geometry restraints manager: 2.07 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: 12442 20.36 - 40.72: 593 40.72 - 61.08: 185 61.08 - 81.44: 37 81.44 - 101.80: 7 Dihedral angle restraints: 13264 sinusoidal: 5437 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 13261 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.480 Find NCS groups from input model: 0.550 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 14.064 101.803 8146 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 : 0.809 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: 0.1760 time to fit residues: 181.2419 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 : 0.849 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3550 r_free = 0.3550 target = 0.141022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111339 restraints weight = 28415.741| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.00 r_work: 0.3054 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2674 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= 0.149 Angle : 0.618 9.082 29714 Z= 0.320 Chirality : 0.042 0.224 3393 Planarity : 0.005 0.059 3668 Dihedral : 11.394 59.962 3411 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.53 % Allowed : 11.14 % 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: -2.14 (0.14), residues: 2601 helix: -0.76 (0.11), residues: 1844 sheet: None (None), residues: 0 loop : -2.86 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 71 TYR 0.022 0.001 TYR A 523 PHE 0.027 0.002 PHE B 378 TRP 0.018 0.001 TRP D 314 HIS 0.003 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (21899) covalent geometry : angle 0.61699 / 0.32 (29706) SS BOND : bond 0.00717 / 0.36 ( 4) SS BOND : angle 1.93381 / 1.23 ( 8) hydrogen bonds : bond 0.04370 / 2.90 ( 1277) hydrogen bonds : angle 4.41961 / 3.13 ( 3720) Misc. bond : bond 0.00447 / 0.23 ( 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 559 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 481 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 ASP cc_start: 0.8799 (m-30) cc_final: 0.8598 (m-30) REVERT: A 257 ASP cc_start: 0.8266 (m-30) cc_final: 0.8030 (m-30) REVERT: A 323 ARG cc_start: 0.7490 (mtt180) cc_final: 0.7082 (tpt170) REVERT: A 505 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 556 LYS cc_start: 0.8663 (tptt) cc_final: 0.8114 (tptp) REVERT: A 615 MET cc_start: 0.8734 (mtt) cc_final: 0.8485 (mtt) REVERT: A 619 MET cc_start: 0.8993 (ttp) cc_final: 0.8655 (ttp) REVERT: B 50 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7887 (mmtm) REVERT: B 79 GLU cc_start: 0.8288 (tt0) cc_final: 0.8055 (tt0) REVERT: B 246 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8147 (ttp-110) REVERT: B 272 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7625 (ttp80) REVERT: B 339 LEU cc_start: 0.8696 (mt) cc_final: 0.8382 (mt) REVERT: B 405 MET cc_start: 0.7328 (mtp) cc_final: 0.6535 (mtp) REVERT: B 409 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.7328 (m-90) REVERT: B 453 ILE cc_start: 0.8074 (mm) cc_final: 0.7726 (mm) REVERT: B 456 PHE cc_start: 0.7978 (t80) cc_final: 0.7616 (t80) REVERT: B 471 TRP cc_start: 0.8641 (m100) cc_final: 0.8110 (m-10) REVERT: B 532 ASN cc_start: 0.8665 (m-40) cc_final: 0.8357 (m-40) REVERT: B 563 THR cc_start: 0.8908 (p) cc_final: 0.8678 (t) REVERT: B 619 MET cc_start: 0.9074 (ttm) cc_final: 0.8798 (ttp) REVERT: B 621 ASN cc_start: 0.8608 (m110) cc_final: 0.8183 (m-40) REVERT: B 634 GLU cc_start: 0.8374 (tt0) cc_final: 0.7968 (mt-10) REVERT: B 737 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7517 (mmmt) REVERT: C 34 LYS cc_start: 0.8487 (mttt) cc_final: 0.7894 (mmtt) REVERT: C 228 GLN cc_start: 0.8130 (tp40) cc_final: 0.7913 (mm-40) REVERT: C 272 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6631 (ttp80) REVERT: C 403 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5849 (mt-10) REVERT: C 405 MET cc_start: 0.7528 (mtp) cc_final: 0.6591 (mtp) REVERT: C 409 TRP cc_start: 0.8587 (OUTLIER) cc_final: 0.7409 (m-90) REVERT: C 453 ILE cc_start: 0.8148 (mm) cc_final: 0.7761 (mm) REVERT: C 505 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8478 (tp) REVERT: C 532 ASN cc_start: 0.8710 (m-40) cc_final: 0.8477 (m-40) REVERT: C 563 THR cc_start: 0.8923 (p) cc_final: 0.8584 (t) REVERT: C 583 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.8995 (t) REVERT: C 615 MET cc_start: 0.8872 (mtt) cc_final: 0.8638 (mtt) REVERT: C 737 LYS cc_start: 0.8179 (mmtm) cc_final: 0.7692 (mmmm) REVERT: D 272 ARG cc_start: 0.7131 (ttp80) cc_final: 0.6677 (ttp80) REVERT: D 294 LYS cc_start: 0.8725 (tttm) cc_final: 0.8325 (tmtt) REVERT: D 405 MET cc_start: 0.7301 (mtp) cc_final: 0.6980 (mtp) REVERT: D 419 LYS cc_start: 0.8543 (tptm) cc_final: 0.8262 (ttmt) REVERT: D 532 ASN cc_start: 0.8866 (m-40) cc_final: 0.8458 (m-40) REVERT: D 619 MET cc_start: 0.9043 (ttm) cc_final: 0.8765 (ttp) REVERT: D 634 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: D 703 HIS cc_start: 0.7834 (t70) cc_final: 0.7595 (t70) REVERT: D 737 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7592 (mmmm) outliers start: 78 outliers final: 43 residues processed: 539 average time/residue: 0.1525 time to fit residues: 127.9166 Evaluate side-chains 438 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 387 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 B residue 741 GLN 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 65 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 377 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: 0.5980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 239 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 154 ASN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3621 r_free = 0.3621 target = 0.146569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118122 restraints weight = 27896.675| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.91 r_work: 0.3032 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21906 Z= 0.138 Angle : 0.556 9.437 29714 Z= 0.289 Chirality : 0.042 0.349 3393 Planarity : 0.004 0.054 3668 Dihedral : 10.316 59.906 3335 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 3.71 % Allowed : 13.68 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2601 helix: 0.38 (0.12), residues: 1867 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 734 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 0.030 0.002 PHE A 378 TRP 0.014 0.001 TRP B 314 HIS 0.002 0.000 HIS A 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (21899) covalent geometry : angle 0.55472 / 0.29 (29706) SS BOND : bond 0.00860 / 0.43 ( 4) SS BOND : angle 2.11573 / 1.75 ( 8) hydrogen bonds : bond 0.04016 / 2.66 ( 1277) hydrogen bonds : angle 3.91154 / 2.78 ( 3720) Misc. bond : bond 0.00536 / 0.28 ( 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 516 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 434 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8274 (pt) REVERT: A 194 ARG cc_start: 0.8439 (tpp-160) cc_final: 0.8200 (tpp80) REVERT: A 254 ASP cc_start: 0.8737 (m-30) cc_final: 0.8492 (m-30) REVERT: A 323 ARG cc_start: 0.7386 (mtt180) cc_final: 0.7172 (tpt170) REVERT: A 339 LEU cc_start: 0.8894 (mt) cc_final: 0.8638 (mp) REVERT: A 419 LYS cc_start: 0.8654 (tptm) cc_final: 0.8441 (ttmt) REVERT: A 420 GLN cc_start: 0.7935 (tt0) cc_final: 0.7495 (tt0) REVERT: A 471 TRP cc_start: 0.8461 (m100) cc_final: 0.8143 (m100) REVERT: A 505 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 538 TYR cc_start: 0.8807 (m-80) cc_final: 0.8599 (m-80) REVERT: A 615 MET cc_start: 0.8636 (mtt) cc_final: 0.8424 (mtt) REVERT: B 47 SER cc_start: 0.8358 (t) cc_final: 0.8153 (t) REVERT: B 50 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7623 (mmtp) REVERT: B 79 GLU cc_start: 0.8373 (tt0) cc_final: 0.8037 (tt0) REVERT: B 88 LEU cc_start: 0.8760 (tp) cc_final: 0.8559 (tp) REVERT: B 194 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8125 (tpp80) REVERT: B 272 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.7637 (ttp80) REVERT: B 405 MET cc_start: 0.7143 (mtp) cc_final: 0.6270 (mtp) REVERT: B 409 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.7315 (m-90) REVERT: B 420 GLN cc_start: 0.7973 (tt0) cc_final: 0.7738 (tt0) REVERT: B 453 ILE cc_start: 0.8190 (mm) cc_final: 0.7824 (mm) REVERT: B 456 PHE cc_start: 0.7908 (t80) cc_final: 0.7580 (t80) REVERT: B 532 ASN cc_start: 0.8603 (m-40) cc_final: 0.8344 (m-40) REVERT: B 619 MET cc_start: 0.9096 (ttm) cc_final: 0.8748 (ttp) REVERT: B 737 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7540 (mmmt) REVERT: C 194 ARG cc_start: 0.8378 (tpp80) cc_final: 0.8108 (tpp-160) REVERT: C 272 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6572 (ttp80) REVERT: C 403 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5713 (tp30) REVERT: C 405 MET cc_start: 0.7334 (mtp) cc_final: 0.6579 (mtp) REVERT: C 409 TRP cc_start: 0.8634 (OUTLIER) cc_final: 0.7354 (m-90) REVERT: C 505 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 532 ASN cc_start: 0.8570 (m-40) cc_final: 0.8308 (m-40) REVERT: C 619 MET cc_start: 0.8938 (ttp) cc_final: 0.8712 (ttm) REVERT: C 737 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7621 (mmmm) REVERT: D 272 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6745 (ttp80) REVERT: D 294 LYS cc_start: 0.8826 (tttm) cc_final: 0.8414 (tmtt) REVERT: D 405 MET cc_start: 0.7227 (mtp) cc_final: 0.6560 (mtp) REVERT: D 409 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7139 (m-90) REVERT: D 532 ASN cc_start: 0.8851 (m-40) cc_final: 0.8278 (m-40) REVERT: D 536 GLN cc_start: 0.9150 (tp40) cc_final: 0.8520 (tp40) REVERT: D 583 VAL cc_start: 0.9272 (OUTLIER) cc_final: 0.8982 (t) REVERT: D 619 MET cc_start: 0.8991 (ttm) cc_final: 0.8599 (ttp) REVERT: D 648 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7698 (pt0) REVERT: D 737 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7509 (mmmm) outliers start: 82 outliers final: 40 residues processed: 482 average time/residue: 0.1463 time to fit residues: 110.5578 Evaluate side-chains 435 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 386 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 514 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 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 407 LEU 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 549 CYS 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 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 451 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 633 ILE 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: 5.9990 chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 82 optimal weight: 0.0370 chunk 126 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 chunk 143 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 82 ASN 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 ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 741 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.144294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114840 restraints weight = 28078.680| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.96 r_work: 0.3028 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21906 Z= 0.121 Angle : 0.526 10.487 29714 Z= 0.273 Chirality : 0.041 0.388 3393 Planarity : 0.004 0.053 3668 Dihedral : 9.851 59.891 3333 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.44 % Allowed : 14.49 % Favored : 81.07 % 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: 0.08 (0.16), residues: 2601 helix: 0.97 (0.12), residues: 1877 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 296 TYR 0.020 0.001 TYR A 523 PHE 0.023 0.001 PHE C 340 TRP 0.012 0.001 TRP B 635 HIS 0.002 0.000 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21899) covalent geometry : angle 0.52512 / 0.27 (29706) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 2.22035 / 1.52 ( 8) hydrogen bonds : bond 0.03782 / 2.51 ( 1277) hydrogen bonds : angle 3.65691 / 2.61 ( 3720) Misc. bond : bond 0.00048 / 0.02 ( 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 531 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 433 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8272 (pt) REVERT: A 194 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.8124 (tpp80) REVERT: A 215 ASP cc_start: 0.8301 (p0) cc_final: 0.7800 (p0) REVERT: A 420 GLN cc_start: 0.7895 (tt0) cc_final: 0.7466 (tt0) REVERT: A 505 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 538 TYR cc_start: 0.8777 (m-80) cc_final: 0.8470 (m-80) REVERT: A 634 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: A 648 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7910 (pt0) REVERT: B 50 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7870 (mmtp) REVERT: B 194 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8166 (tpp80) REVERT: B 243 GLU cc_start: 0.8356 (tt0) cc_final: 0.8034 (pt0) REVERT: B 272 ARG cc_start: 0.7856 (tpp-160) cc_final: 0.7461 (ttp80) REVERT: B 340 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8150 (p90) REVERT: B 405 MET cc_start: 0.7193 (mtp) cc_final: 0.6206 (mtp) REVERT: B 409 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.7260 (m-90) REVERT: B 420 GLN cc_start: 0.7962 (tt0) cc_final: 0.7712 (tt0) REVERT: B 453 ILE cc_start: 0.8143 (mm) cc_final: 0.7796 (mm) REVERT: B 456 PHE cc_start: 0.7698 (t80) cc_final: 0.7324 (t80) REVERT: B 532 ASN cc_start: 0.8560 (m-40) cc_final: 0.8224 (m-40) REVERT: B 583 VAL cc_start: 0.9347 (OUTLIER) cc_final: 0.9052 (t) REVERT: B 619 MET cc_start: 0.9045 (ttm) cc_final: 0.8676 (ttp) REVERT: B 737 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7503 (mmmm) REVERT: C 194 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8016 (tpp-160) REVERT: C 272 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6579 (ttp80) REVERT: C 403 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5791 (tp30) REVERT: C 405 MET cc_start: 0.7318 (mtp) cc_final: 0.6523 (mtp) REVERT: C 409 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.7334 (m-90) REVERT: C 420 GLN cc_start: 0.8009 (tt0) cc_final: 0.7719 (tt0) REVERT: C 456 PHE cc_start: 0.7915 (t80) cc_final: 0.7373 (t80) REVERT: C 505 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8513 (tp) REVERT: C 532 ASN cc_start: 0.8591 (m-40) cc_final: 0.8389 (t0) REVERT: C 583 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9101 (t) REVERT: C 737 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7636 (mmmm) REVERT: D 113 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7931 (mt-10) REVERT: D 215 ASP cc_start: 0.8178 (p0) cc_final: 0.7735 (p0) REVERT: D 272 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6816 (ttp80) REVERT: D 294 LYS cc_start: 0.8860 (tttm) cc_final: 0.8466 (tmtt) REVERT: D 409 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.7143 (m-90) REVERT: D 420 GLN cc_start: 0.8056 (tt0) cc_final: 0.7779 (tt0) REVERT: D 456 PHE cc_start: 0.7747 (t80) cc_final: 0.7329 (t80) REVERT: D 583 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.9057 (t) REVERT: D 619 MET cc_start: 0.8961 (ttm) cc_final: 0.8616 (ttp) REVERT: D 737 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7543 (mmmm) outliers start: 98 outliers final: 42 residues processed: 498 average time/residue: 0.1493 time to fit residues: 116.7527 Evaluate side-chains 458 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 403 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 224 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 421 MET 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 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 437 MET Chi-restraints excluded: chain B residue 505 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 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 C residue 633 ILE 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 379 LEU Chi-restraints excluded: chain D residue 406 ILE 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 Chi-restraints excluded: chain D residue 700 LEU 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: 1.9990 chunk 186 optimal weight: 0.0970 chunk 250 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN 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 442 ASN C 506 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107896 restraints weight = 28224.357| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.05 r_work: 0.2991 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21906 Z= 0.127 Angle : 0.527 10.915 29714 Z= 0.273 Chirality : 0.041 0.359 3393 Planarity : 0.004 0.053 3668 Dihedral : 9.664 59.975 3333 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.94 % Allowed : 15.94 % Favored : 80.12 % 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: 0.47 (0.16), residues: 2601 helix: 1.27 (0.12), residues: 1883 sheet: None (None), residues: 0 loop : -2.32 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 296 TYR 0.020 0.001 TYR C 523 PHE 0.024 0.002 PHE C 340 TRP 0.011 0.001 TRP B 314 HIS 0.001 0.000 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21899) covalent geometry : angle 0.52633 / 0.27 (29706) SS BOND : bond 0.00254 / 0.13 ( 4) SS BOND : angle 2.05264 / 1.37 ( 8) hydrogen bonds : bond 0.03750 / 2.50 ( 1277) hydrogen bonds : angle 3.56967 / 2.54 ( 3720) Misc. bond : bond 0.00188 / 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 511 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 424 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8242 (pt) REVERT: A 194 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.8171 (tpp80) REVERT: A 215 ASP cc_start: 0.8251 (p0) cc_final: 0.7778 (p0) REVERT: A 420 GLN cc_start: 0.7921 (tt0) cc_final: 0.7553 (tt0) REVERT: A 505 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 538 TYR cc_start: 0.8873 (m-80) cc_final: 0.8625 (m-80) REVERT: A 558 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 648 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7923 (pt0) REVERT: B 50 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7947 (mmtp) REVERT: B 194 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8149 (tpp80) REVERT: B 243 GLU cc_start: 0.8377 (tt0) cc_final: 0.8050 (pt0) REVERT: B 272 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7439 (ttp80) REVERT: B 340 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8112 (p90) REVERT: B 405 MET cc_start: 0.7600 (mtp) cc_final: 0.6699 (mtp) REVERT: B 409 TRP cc_start: 0.8685 (OUTLIER) cc_final: 0.7304 (m-90) REVERT: B 420 GLN cc_start: 0.7986 (tt0) cc_final: 0.7689 (tt0) REVERT: B 453 ILE cc_start: 0.8140 (mm) cc_final: 0.7783 (mm) REVERT: B 456 PHE cc_start: 0.7713 (t80) cc_final: 0.7319 (t80) REVERT: B 532 ASN cc_start: 0.8590 (m-40) cc_final: 0.8370 (t0) REVERT: B 535 ASN cc_start: 0.9316 (t0) cc_final: 0.9073 (t0) REVERT: B 583 VAL cc_start: 0.9368 (OUTLIER) cc_final: 0.9089 (t) REVERT: B 619 MET cc_start: 0.9015 (ttm) cc_final: 0.8663 (ttp) REVERT: B 737 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7408 (mmmm) REVERT: C 79 GLU cc_start: 0.8262 (tt0) cc_final: 0.7932 (tt0) REVERT: C 194 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8076 (tpp-160) REVERT: C 215 ASP cc_start: 0.8350 (p0) cc_final: 0.7805 (p0) REVERT: C 272 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6769 (ttp80) REVERT: C 331 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8767 (t) REVERT: C 403 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.6060 (tp30) REVERT: C 405 MET cc_start: 0.7468 (mtp) cc_final: 0.6744 (mtp) REVERT: C 409 TRP cc_start: 0.8664 (OUTLIER) cc_final: 0.7405 (m-90) REVERT: C 505 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (tp) REVERT: C 583 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9136 (t) REVERT: C 737 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7612 (mmmm) REVERT: D 215 ASP cc_start: 0.8247 (p0) cc_final: 0.7779 (p0) REVERT: D 272 ARG cc_start: 0.7327 (ttp80) cc_final: 0.6924 (ttp80) REVERT: D 294 LYS cc_start: 0.8965 (tttm) cc_final: 0.8537 (tmtt) REVERT: D 405 MET cc_start: 0.7609 (mtp) cc_final: 0.6821 (mtp) REVERT: D 409 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7141 (m-90) REVERT: D 419 LYS cc_start: 0.8449 (tptm) cc_final: 0.8205 (ttmt) REVERT: D 456 PHE cc_start: 0.7821 (t80) cc_final: 0.7402 (t80) REVERT: D 536 GLN cc_start: 0.9208 (tp40) cc_final: 0.8480 (tp40) REVERT: D 583 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9057 (t) REVERT: D 619 MET cc_start: 0.8948 (ttm) cc_final: 0.8660 (ttp) REVERT: D 737 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7514 (mmmm) outliers start: 87 outliers final: 42 residues processed: 474 average time/residue: 0.1501 time to fit residues: 112.1328 Evaluate side-chains 456 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 400 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 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 331 VAL 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 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 379 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: 4.9990 chunk 152 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 206 optimal weight: 0.0020 chunk 215 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 0.0470 chunk 187 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN D 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108804 restraints weight = 28193.071| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.03 r_work: 0.3029 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4076 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= 0.116 Angle : 0.519 11.156 29714 Z= 0.269 Chirality : 0.041 0.412 3393 Planarity : 0.004 0.052 3668 Dihedral : 9.366 59.483 3329 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.49 % Allowed : 16.12 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2601 helix: 1.48 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 296 TYR 0.019 0.001 TYR C 523 PHE 0.025 0.001 PHE A 378 TRP 0.026 0.001 TRP A 409 HIS 0.002 0.000 HIS C 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21899) covalent geometry : angle 0.51640 / 0.27 (29706) SS BOND : bond 0.00478 / 0.23 ( 4) SS BOND : angle 3.38445 / 1.83 ( 8) hydrogen bonds : bond 0.03599 / 2.39 ( 1277) hydrogen bonds : angle 3.47689 / 2.46 ( 3720) Misc. bond : bond 0.00320 / 0.17 ( 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 514 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 437 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8229 (pt) REVERT: A 194 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.8160 (tpp80) REVERT: A 215 ASP cc_start: 0.8104 (p0) cc_final: 0.7682 (p0) REVERT: A 339 LEU cc_start: 0.9074 (mt) cc_final: 0.8792 (mt) REVERT: A 405 MET cc_start: 0.7465 (mtp) cc_final: 0.7070 (mtm) REVERT: A 419 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8166 (mtpp) REVERT: A 420 GLN cc_start: 0.7823 (tt0) cc_final: 0.7443 (tt0) REVERT: A 470 MET cc_start: 0.7836 (tmm) cc_final: 0.7500 (tmm) REVERT: A 505 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8480 (tp) REVERT: A 538 TYR cc_start: 0.8914 (m-80) cc_final: 0.8654 (m-80) REVERT: A 558 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7981 (p0) REVERT: A 583 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9089 (t) REVERT: B 50 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7184 (mmtp) REVERT: B 54 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 79 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 243 GLU cc_start: 0.8370 (tt0) cc_final: 0.8062 (pt0) REVERT: B 272 ARG cc_start: 0.7878 (tpp-160) cc_final: 0.7481 (ttp80) REVERT: B 340 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8059 (p90) REVERT: B 401 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7110 (tp) REVERT: B 405 MET cc_start: 0.7620 (mtp) cc_final: 0.6638 (mtp) REVERT: B 409 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.7256 (m-90) REVERT: B 420 GLN cc_start: 0.7999 (tt0) cc_final: 0.7605 (tt0) REVERT: B 453 ILE cc_start: 0.8204 (mm) cc_final: 0.7872 (mm) REVERT: B 532 ASN cc_start: 0.8595 (m-40) cc_final: 0.8323 (t0) REVERT: B 535 ASN cc_start: 0.9314 (t0) cc_final: 0.9094 (t0) REVERT: B 583 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9107 (t) REVERT: B 619 MET cc_start: 0.8929 (ttm) cc_final: 0.8571 (ttp) REVERT: B 737 LYS cc_start: 0.7902 (mmtm) cc_final: 0.7400 (mmmm) REVERT: C 38 ASN cc_start: 0.8571 (t0) cc_final: 0.7965 (t0) REVERT: C 42 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8029 (mtmt) REVERT: C 44 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: C 79 GLU cc_start: 0.8242 (tt0) cc_final: 0.8019 (tt0) REVERT: C 113 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7661 (mt-10) REVERT: C 194 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8096 (tpp-160) REVERT: C 215 ASP cc_start: 0.8314 (p0) cc_final: 0.7815 (p0) REVERT: C 243 GLU cc_start: 0.8396 (tt0) cc_final: 0.8049 (pt0) REVERT: C 272 ARG cc_start: 0.7304 (ttp80) cc_final: 0.6832 (ttp80) REVERT: C 405 MET cc_start: 0.7421 (mtp) cc_final: 0.6630 (mtp) REVERT: C 409 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.7275 (m-90) REVERT: C 470 MET cc_start: 0.7708 (tmm) cc_final: 0.7419 (tmm) REVERT: C 505 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8507 (tp) REVERT: C 536 GLN cc_start: 0.8839 (tp40) cc_final: 0.8608 (tp40) REVERT: C 583 VAL cc_start: 0.9423 (OUTLIER) cc_final: 0.9133 (t) REVERT: C 737 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7562 (mmmm) REVERT: D 215 ASP cc_start: 0.8204 (p0) cc_final: 0.7754 (p0) REVERT: D 272 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7005 (ttp80) REVERT: D 294 LYS cc_start: 0.8966 (tttm) cc_final: 0.8550 (tmtt) REVERT: D 401 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7017 (tp) REVERT: D 405 MET cc_start: 0.7625 (mtp) cc_final: 0.6783 (mtp) REVERT: D 409 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.7160 (m-90) REVERT: D 419 LYS cc_start: 0.8477 (tptm) cc_final: 0.8225 (ttmt) REVERT: D 442 ASN cc_start: 0.8903 (m-40) cc_final: 0.8659 (m110) REVERT: D 456 PHE cc_start: 0.7792 (t80) cc_final: 0.7368 (t80) REVERT: D 536 GLN cc_start: 0.9203 (tp40) cc_final: 0.8548 (tp40) REVERT: D 583 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9051 (t) REVERT: D 619 MET cc_start: 0.8867 (ttm) cc_final: 0.8591 (ttp) REVERT: D 737 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7546 (mmmm) outliers start: 77 outliers final: 42 residues processed: 486 average time/residue: 0.1484 time to fit residues: 113.1172 Evaluate side-chains 471 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 412 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 422 TRP 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 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 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 379 LEU 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 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 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 401 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 180 optimal weight: 0.0270 chunk 146 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109682 restraints weight = 28278.762| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.04 r_work: 0.2995 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4249 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= 0.115 Angle : 0.514 11.240 29714 Z= 0.266 Chirality : 0.041 0.353 3393 Planarity : 0.004 0.050 3668 Dihedral : 8.985 59.871 3327 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.53 % Allowed : 16.03 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2601 helix: 1.61 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -2.10 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 296 TYR 0.018 0.001 TYR C 523 PHE 0.028 0.001 PHE B 456 TRP 0.022 0.001 TRP A 409 HIS 0.002 0.000 HIS D 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (21899) covalent geometry : angle 0.51193 / 0.26 (29706) SS BOND : bond 0.00170 / 0.09 ( 4) SS BOND : angle 2.97948 / 1.63 ( 8) hydrogen bonds : bond 0.03561 / 2.36 ( 1277) hydrogen bonds : angle 3.43267 / 2.43 ( 3720) Misc. bond : bond 0.00165 / 0.09 ( 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 509 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 431 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8231 (pt) REVERT: A 194 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.8124 (tpp80) REVERT: A 215 ASP cc_start: 0.8056 (p0) cc_final: 0.7782 (p0) REVERT: A 294 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8704 (tptt) REVERT: A 405 MET cc_start: 0.7664 (mtp) cc_final: 0.7153 (mtm) REVERT: A 420 GLN cc_start: 0.7807 (tt0) cc_final: 0.7334 (tt0) REVERT: A 470 MET cc_start: 0.7816 (tmm) cc_final: 0.7465 (tmm) REVERT: A 505 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 558 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 583 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9089 (t) REVERT: B 50 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7045 (mmtp) REVERT: B 54 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: B 79 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 215 ASP cc_start: 0.8109 (p0) cc_final: 0.7566 (p0) REVERT: B 243 GLU cc_start: 0.8337 (tt0) cc_final: 0.8014 (pt0) REVERT: B 272 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7399 (ttp80) REVERT: B 340 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7926 (p90) REVERT: B 401 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7044 (tp) REVERT: B 405 MET cc_start: 0.7759 (mtp) cc_final: 0.6410 (mtm) REVERT: B 409 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.7162 (m-90) REVERT: B 420 GLN cc_start: 0.7989 (tt0) cc_final: 0.7647 (tt0) REVERT: B 456 PHE cc_start: 0.7937 (t80) cc_final: 0.7613 (t80) REVERT: B 532 ASN cc_start: 0.8559 (m-40) cc_final: 0.8289 (t0) REVERT: B 583 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9133 (t) REVERT: B 737 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7327 (mmmm) REVERT: C 79 GLU cc_start: 0.8268 (tt0) cc_final: 0.7989 (tt0) REVERT: C 215 ASP cc_start: 0.8291 (p0) cc_final: 0.7814 (p0) REVERT: C 243 GLU cc_start: 0.8356 (tt0) cc_final: 0.8009 (pt0) REVERT: C 272 ARG cc_start: 0.7071 (ttp80) cc_final: 0.6725 (ttp80) REVERT: C 335 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8761 (pt) REVERT: C 405 MET cc_start: 0.7695 (mtp) cc_final: 0.6444 (mtm) REVERT: C 409 TRP cc_start: 0.8619 (OUTLIER) cc_final: 0.7279 (m-90) REVERT: C 420 GLN cc_start: 0.8008 (tt0) cc_final: 0.7805 (tt0) REVERT: C 470 MET cc_start: 0.7591 (tmm) cc_final: 0.7314 (tmm) REVERT: C 505 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8423 (tp) REVERT: C 536 GLN cc_start: 0.8914 (tp40) cc_final: 0.8676 (tp40) REVERT: C 583 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9144 (t) REVERT: C 737 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7524 (mmmm) REVERT: D 215 ASP cc_start: 0.8165 (p0) cc_final: 0.7709 (p0) REVERT: D 272 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6996 (ttp80) REVERT: D 294 LYS cc_start: 0.8940 (tttm) cc_final: 0.8505 (tmtt) REVERT: D 405 MET cc_start: 0.7733 (mtp) cc_final: 0.6686 (mtp) REVERT: D 409 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.7152 (m-90) REVERT: D 419 LYS cc_start: 0.8489 (tptm) cc_final: 0.8228 (ttmt) REVERT: D 442 ASN cc_start: 0.8879 (m-40) cc_final: 0.8658 (m110) REVERT: D 456 PHE cc_start: 0.7768 (t80) cc_final: 0.7354 (t80) REVERT: D 583 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9053 (t) REVERT: D 737 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7531 (mmmm) outliers start: 78 outliers final: 45 residues processed: 479 average time/residue: 0.1494 time to fit residues: 112.0497 Evaluate side-chains 470 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 409 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain A residue 442 ASN 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 409 TRP Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 442 ASN 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 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 335 ILE 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 437 MET Chi-restraints excluded: chain C residue 442 ASN 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 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 379 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 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 750 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 535 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114652 restraints weight = 28000.924| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.95 r_work: 0.3046 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4306 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= 0.145 Angle : 0.546 10.445 29714 Z= 0.282 Chirality : 0.042 0.347 3393 Planarity : 0.004 0.049 3668 Dihedral : 8.909 59.663 3327 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.40 % Allowed : 16.94 % Favored : 79.66 % 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: 1888 sheet: None (None), residues: 0 loop : -2.05 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 296 TYR 0.021 0.001 TYR C 523 PHE 0.028 0.002 PHE D 340 TRP 0.021 0.001 TRP A 468 HIS 0.002 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (21899) covalent geometry : angle 0.54475 / 0.28 (29706) SS BOND : bond 0.00160 / 0.08 ( 4) SS BOND : angle 2.45814 / 1.48 ( 8) hydrogen bonds : bond 0.03730 / 2.48 ( 1277) hydrogen bonds : angle 3.51139 / 2.48 ( 3720) Misc. bond : bond 0.00281 / 0.15 ( 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 488 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 413 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8301 (pt) REVERT: A 215 ASP cc_start: 0.8086 (p0) cc_final: 0.7797 (p0) REVERT: A 294 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8645 (tptt) REVERT: A 405 MET cc_start: 0.7728 (mtp) cc_final: 0.7161 (mtm) REVERT: A 505 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 558 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8034 (p0) REVERT: B 50 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7092 (mmtp) REVERT: B 54 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: B 79 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7805 (mt-10) REVERT: B 215 ASP cc_start: 0.8130 (p0) cc_final: 0.7831 (p0) REVERT: B 243 GLU cc_start: 0.8377 (tt0) cc_final: 0.8069 (pt0) REVERT: B 272 ARG cc_start: 0.7926 (tpp-160) cc_final: 0.7540 (ttp80) REVERT: B 401 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7179 (tp) REVERT: B 405 MET cc_start: 0.7822 (mtp) cc_final: 0.6800 (mtp) REVERT: B 409 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.7297 (m-90) REVERT: B 420 GLN cc_start: 0.8097 (tt0) cc_final: 0.7830 (tt0) REVERT: B 456 PHE cc_start: 0.7907 (t80) cc_final: 0.7590 (t80) REVERT: B 532 ASN cc_start: 0.8617 (m-40) cc_final: 0.8379 (t0) REVERT: B 556 LYS cc_start: 0.8104 (tptt) cc_final: 0.7901 (tptt) REVERT: B 583 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9136 (t) REVERT: B 721 MET cc_start: 0.8769 (mmt) cc_final: 0.8461 (mmp) REVERT: B 737 LYS cc_start: 0.7945 (mmtm) cc_final: 0.7535 (mmmm) REVERT: C 79 GLU cc_start: 0.8291 (tt0) cc_final: 0.8017 (tt0) REVERT: C 215 ASP cc_start: 0.8349 (p0) cc_final: 0.7849 (p0) REVERT: C 272 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6945 (ttp80) REVERT: C 335 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8771 (pt) REVERT: C 405 MET cc_start: 0.7757 (mtp) cc_final: 0.6591 (mtm) REVERT: C 409 TRP cc_start: 0.8653 (OUTLIER) cc_final: 0.7418 (m-90) REVERT: C 470 MET cc_start: 0.7606 (tmm) cc_final: 0.7351 (tmm) REVERT: C 505 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (tp) REVERT: C 536 GLN cc_start: 0.8908 (tp40) cc_final: 0.8656 (tp40) REVERT: C 583 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.9180 (t) REVERT: C 737 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7930 (mmmm) REVERT: D 215 ASP cc_start: 0.8218 (p0) cc_final: 0.7785 (p0) REVERT: D 272 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7125 (ttp80) REVERT: D 294 LYS cc_start: 0.8948 (tttm) cc_final: 0.8547 (tmtt) REVERT: D 405 MET cc_start: 0.7776 (mtp) cc_final: 0.6419 (mtm) REVERT: D 409 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7122 (m-90) REVERT: D 456 PHE cc_start: 0.7812 (t80) cc_final: 0.7343 (t80) REVERT: D 536 GLN cc_start: 0.9195 (tp40) cc_final: 0.8443 (tp40) REVERT: D 737 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7662 (mmmm) outliers start: 75 outliers final: 49 residues processed: 463 average time/residue: 0.1454 time to fit residues: 106.6325 Evaluate side-chains 455 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 393 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 381 LEU Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 563 THR 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 437 MET Chi-restraints excluded: chain B residue 442 ASN Chi-restraints excluded: chain B residue 505 LEU 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 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 335 ILE 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 442 ASN 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 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 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 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: 4.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 256 optimal weight: 0.1980 chunk 180 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN D 442 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.139218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108394 restraints weight = 28092.308| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.03 r_work: 0.2980 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21906 Z= 0.124 Angle : 0.536 10.262 29714 Z= 0.277 Chirality : 0.041 0.305 3393 Planarity : 0.004 0.050 3668 Dihedral : 8.793 59.663 3327 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 3.03 % Allowed : 17.98 % Favored : 78.99 % 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: 1.06 (0.17), residues: 2601 helix: 1.66 (0.12), residues: 1888 sheet: None (None), residues: 0 loop : -2.00 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 296 TYR 0.019 0.001 TYR C 523 PHE 0.028 0.001 PHE D 340 TRP 0.016 0.001 TRP C 326 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (21899) covalent geometry : angle 0.53437 / 0.28 (29706) SS BOND : bond 0.00155 / 0.08 ( 4) SS BOND : angle 2.37177 / 1.39 ( 8) hydrogen bonds : bond 0.03615 / 2.39 ( 1277) hydrogen bonds : angle 3.51428 / 2.47 ( 3720) Misc. bond : bond 0.00336 / 0.18 ( 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 476 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 409 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (pt) REVERT: A 215 ASP cc_start: 0.8017 (p0) cc_final: 0.7715 (p0) REVERT: A 294 LYS cc_start: 0.8962 (tmtt) cc_final: 0.8676 (tptt) REVERT: A 405 MET cc_start: 0.7760 (mtp) cc_final: 0.7167 (mtm) REVERT: A 419 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8099 (ttmt) REVERT: A 505 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8468 (tp) REVERT: A 558 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8241 (p0) REVERT: A 583 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9145 (t) REVERT: B 50 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7102 (mmtp) REVERT: B 54 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 79 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 215 ASP cc_start: 0.8049 (p0) cc_final: 0.7726 (p0) REVERT: B 243 GLU cc_start: 0.8323 (tt0) cc_final: 0.7995 (pt0) REVERT: B 272 ARG cc_start: 0.7822 (tpp-160) cc_final: 0.7459 (ttp80) REVERT: B 401 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7152 (tp) REVERT: B 405 MET cc_start: 0.7875 (mtp) cc_final: 0.6786 (mtp) REVERT: B 409 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.7209 (m-90) REVERT: B 420 GLN cc_start: 0.8045 (tt0) cc_final: 0.7827 (tt0) REVERT: B 442 ASN cc_start: 0.8931 (OUTLIER) cc_final: 0.8729 (m110) REVERT: B 456 PHE cc_start: 0.7935 (t80) cc_final: 0.7621 (t80) REVERT: B 532 ASN cc_start: 0.8562 (m-40) cc_final: 0.8306 (t0) REVERT: B 556 LYS cc_start: 0.8093 (tptt) cc_final: 0.7889 (tptt) REVERT: B 583 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9139 (t) REVERT: B 634 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: B 721 MET cc_start: 0.8730 (mmt) cc_final: 0.8405 (mmp) REVERT: B 737 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7480 (mmmm) REVERT: C 41 GLU cc_start: 0.8145 (tt0) cc_final: 0.7901 (pt0) REVERT: C 79 GLU cc_start: 0.8282 (tt0) cc_final: 0.7994 (tt0) REVERT: C 215 ASP cc_start: 0.8298 (p0) cc_final: 0.7821 (p0) REVERT: C 272 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6787 (ttp80) REVERT: C 294 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8697 (tptt) REVERT: C 335 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8763 (pt) REVERT: C 405 MET cc_start: 0.7807 (mtp) cc_final: 0.6580 (mtm) REVERT: C 409 TRP cc_start: 0.8663 (OUTLIER) cc_final: 0.7393 (m-90) REVERT: C 470 MET cc_start: 0.7716 (tmm) cc_final: 0.7500 (tmm) REVERT: C 505 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 536 GLN cc_start: 0.8944 (tp40) cc_final: 0.8502 (tp40) REVERT: C 583 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9166 (t) REVERT: C 737 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7844 (mmmm) REVERT: D 272 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7032 (ttp80) REVERT: D 294 LYS cc_start: 0.8945 (tttm) cc_final: 0.8514 (tmtt) REVERT: D 405 MET cc_start: 0.7838 (mtp) cc_final: 0.6401 (mtm) REVERT: D 409 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7170 (m-90) REVERT: D 456 PHE cc_start: 0.7854 (t80) cc_final: 0.7355 (t80) REVERT: D 536 GLN cc_start: 0.9201 (tp40) cc_final: 0.8553 (tp40) REVERT: D 583 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9089 (t) REVERT: D 737 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7544 (mmmm) outliers start: 67 outliers final: 43 residues processed: 456 average time/residue: 0.1445 time to fit residues: 104.1987 Evaluate side-chains 454 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 394 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 558 ASN Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 583 VAL 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 406 ILE Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 442 ASN 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 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 335 ILE 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 505 LEU 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 340 PHE 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 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: 4.9990 chunk 1 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 218 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115034 restraints weight = 27833.675| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.94 r_work: 0.3022 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21906 Z= 0.138 Angle : 0.555 11.824 29714 Z= 0.287 Chirality : 0.041 0.273 3393 Planarity : 0.004 0.051 3668 Dihedral : 8.692 59.791 3325 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 2.90 % Allowed : 18.34 % Favored : 78.76 % 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: 1.64 (0.12), residues: 1889 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 296 TYR 0.021 0.001 TYR C 523 PHE 0.028 0.002 PHE D 340 TRP 0.017 0.001 TRP A 468 HIS 0.002 0.000 HIS B 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (21899) covalent geometry : angle 0.55370 / 0.29 (29706) SS BOND : bond 0.00170 / 0.09 ( 4) SS BOND : angle 2.21441 / 1.37 ( 8) hydrogen bonds : bond 0.03712 / 2.46 ( 1277) hydrogen bonds : angle 3.55557 / 2.50 ( 3720) Misc. bond : bond 0.00288 / 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 467 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 403 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (pt) REVERT: A 215 ASP cc_start: 0.8019 (p0) cc_final: 0.7743 (p0) REVERT: A 294 LYS cc_start: 0.8963 (tmtt) cc_final: 0.8662 (tptt) REVERT: A 405 MET cc_start: 0.7793 (mtp) cc_final: 0.7325 (mtm) REVERT: A 505 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (tp) REVERT: A 536 GLN cc_start: 0.9228 (tp40) cc_final: 0.8835 (tp40) REVERT: A 558 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8206 (p0) REVERT: A 733 GLU cc_start: 0.8266 (tt0) cc_final: 0.7934 (tt0) REVERT: B 50 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7178 (mmtp) REVERT: B 54 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: B 79 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 194 ARG cc_start: 0.8562 (tpp-160) cc_final: 0.8258 (tpp80) REVERT: B 215 ASP cc_start: 0.8060 (p0) cc_final: 0.7759 (p0) REVERT: B 243 GLU cc_start: 0.8379 (tt0) cc_final: 0.8049 (pt0) REVERT: B 272 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7560 (ttp80) REVERT: B 294 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8721 (tptt) REVERT: B 401 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7168 (tp) REVERT: B 405 MET cc_start: 0.7934 (mtp) cc_final: 0.6850 (mtp) REVERT: B 409 TRP cc_start: 0.8689 (OUTLIER) cc_final: 0.7240 (m-90) REVERT: B 420 GLN cc_start: 0.8106 (tt0) cc_final: 0.7895 (tt0) REVERT: B 456 PHE cc_start: 0.7878 (t80) cc_final: 0.7557 (t80) REVERT: B 532 ASN cc_start: 0.8573 (m-40) cc_final: 0.8356 (t0) REVERT: B 556 LYS cc_start: 0.8159 (tptt) cc_final: 0.7959 (tptt) REVERT: B 583 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9153 (t) REVERT: B 634 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: B 721 MET cc_start: 0.8747 (mmt) cc_final: 0.8403 (mmp) REVERT: B 737 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7745 (mmmm) REVERT: C 79 GLU cc_start: 0.8373 (tt0) cc_final: 0.8101 (tt0) REVERT: C 113 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7488 (pt0) REVERT: C 215 ASP cc_start: 0.8298 (p0) cc_final: 0.7856 (p0) REVERT: C 272 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6908 (ttp80) REVERT: C 294 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8690 (tptt) REVERT: C 335 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8769 (pt) REVERT: C 403 GLU cc_start: 0.6062 (tp30) cc_final: 0.5546 (tp30) REVERT: C 405 MET cc_start: 0.7803 (mtp) cc_final: 0.6876 (mtp) REVERT: C 409 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7423 (m-90) REVERT: C 505 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (tp) REVERT: C 536 GLN cc_start: 0.8941 (tp40) cc_final: 0.8516 (tp40) REVERT: C 558 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8150 (p0) REVERT: C 583 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9196 (t) REVERT: C 737 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7904 (mmmm) REVERT: D 272 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7063 (ttp80) REVERT: D 294 LYS cc_start: 0.8963 (tttm) cc_final: 0.8580 (tmtt) REVERT: D 404 TRP cc_start: 0.8152 (m100) cc_final: 0.7924 (m100) REVERT: D 405 MET cc_start: 0.7829 (mtp) cc_final: 0.6393 (mtm) REVERT: D 409 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7196 (m-90) REVERT: D 420 GLN cc_start: 0.8005 (tt0) cc_final: 0.7699 (tt0) REVERT: D 536 GLN cc_start: 0.9212 (tp40) cc_final: 0.8557 (tp40) REVERT: D 583 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9110 (t) REVERT: D 737 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8009 (mmmm) outliers start: 64 outliers final: 41 residues processed: 450 average time/residue: 0.1436 time to fit residues: 101.6335 Evaluate side-chains 452 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 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 340 PHE 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 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 409 TRP Chi-restraints excluded: chain B residue 442 ASN 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 109 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 335 ILE 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 442 ASN 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 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 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 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 242 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 61 optimal weight: 0.0970 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 386 HIS B 435 ASN C 80 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.137813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106793 restraints weight = 28233.055| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.03 r_work: 0.2968 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21906 Z= 0.160 Angle : 0.736 59.188 29714 Z= 0.422 Chirality : 0.043 0.757 3393 Planarity : 0.005 0.145 3668 Dihedral : 8.715 59.803 3325 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 2.58 % Allowed : 18.98 % Favored : 78.44 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.64 (0.12), residues: 1889 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 712 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 0.027 0.002 PHE D 340 TRP 0.052 0.001 TRP A 409 HIS 0.004 0.000 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21899) covalent geometry : angle 0.73536 / 0.42 (29706) SS BOND : bond 0.00228 / 0.11 ( 4) SS BOND : angle 2.08907 / 1.30 ( 8) hydrogen bonds : bond 0.03804 / 2.50 ( 1277) hydrogen bonds : angle 3.57670 / 2.51 ( 3720) Misc. bond : bond 0.00228 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.97 seconds wall clock time: 98 minutes 25.25 seconds (5905.25 seconds total)