Starting phenix.real_space_refine on Thu Aug 6 14:28:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.cif Found real_map, /net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.map" model { file = "/net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11km_75776/08_2026/11km_75776.cif" } resolution = 2.97 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= 0.014 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 75 5.16 5 C 9720 2.51 5 N 2631 2.21 5 O 2811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15246 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5029 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 41, 'TRANS': 604} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'COA': 1, 'PRX%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: B, C Time building chain proxies: 3.85, per 1000 atoms: 0.25 Number of scatterers: 15246 At special positions: 0 Unit cell: (84.28, 141.04, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 9 15.00 O 2811 8.00 N 2631 7.00 C 9720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 633.8 milliseconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 36.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.586A pdb=" N ASP A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 45 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.533A pdb=" N MET A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.188A pdb=" N ALA A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.537A pdb=" N MET A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.751A pdb=" N ILE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.719A pdb=" N VAL A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.643A pdb=" N MET A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 359 Processing helix chain 'A' and resid 366 through 377 removed outlier: 3.613A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.854A pdb=" N HIS A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 Processing helix chain 'A' and resid 620 through 629 removed outlier: 4.290A pdb=" N LEU A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.586A pdb=" N ASP B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.533A pdb=" N MET B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 92 through 99 removed outlier: 4.188A pdb=" N ALA B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.538A pdb=" N MET B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 165 removed outlier: 3.750A pdb=" N ILE B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 287 through 301 Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.719A pdb=" N VAL B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.643A pdb=" N MET B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.614A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 409 Processing helix chain 'B' and resid 491 through 499 Processing helix chain 'B' and resid 539 through 549 removed outlier: 3.854A pdb=" N HIS B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 620 through 629 removed outlier: 4.290A pdb=" N LEU B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE B 627 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 661 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.586A pdb=" N ASP C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.532A pdb=" N MET C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 92 through 99 removed outlier: 4.189A pdb=" N ALA C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.537A pdb=" N MET C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.751A pdb=" N ILE C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 189 Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 287 through 301 Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.718A pdb=" N VAL C 326 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.643A pdb=" N MET C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 366 through 377 removed outlier: 3.613A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 539 through 549 removed outlier: 3.854A pdb=" N HIS C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 597 Processing helix chain 'C' and resid 620 through 629 removed outlier: 4.290A pdb=" N LEU C 624 " --> pdb=" O MET C 620 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE C 627 " --> pdb=" O ILE C 623 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 661 Processing sheet with id=1, first strand: chain 'A' and resid 117 through 119 removed outlier: 6.777A pdb=" N ILE A 118 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA A 104 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL A 338 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 106 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS A 312 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE A 339 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 362 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.629A pdb=" N ILE A 193 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 192 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 196 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 145 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS A 169 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N TYR A 272 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL A 171 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 269 " --> pdb=" O HIS A 285 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 285 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 486 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=4, first strand: chain 'A' and resid 390 through 393 removed outlier: 6.496A pdb=" N LEU A 391 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=4 Processing sheet with id=5, first strand: chain 'A' and resid 454 through 457 removed outlier: 6.807A pdb=" N VAL A 470 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA A 512 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 472 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP A 510 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU A 474 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 508 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLY A 509 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG A 525 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 511 " --> pdb=" O ARG A 523 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=7, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.935A pdb=" N LYS A 605 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 117 through 119 removed outlier: 6.777A pdb=" N ILE B 118 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 104 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 338 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 106 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N CYS B 312 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 339 " --> pdb=" O CYS B 312 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 362 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.629A pdb=" N ILE B 193 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 192 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 196 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 145 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 169 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N TYR B 272 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL B 171 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE B 269 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS B 285 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 486 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=11, first strand: chain 'B' and resid 390 through 393 removed outlier: 6.497A pdb=" N LEU B 391 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=11 Processing sheet with id=12, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.806A pdb=" N VAL B 470 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 512 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY B 472 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP B 510 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU B 474 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 508 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLY B 509 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG B 525 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 511 " --> pdb=" O ARG B 523 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 529 through 532 Processing sheet with id=14, first strand: chain 'B' and resid 558 through 560 removed outlier: 3.935A pdb=" N LYS B 605 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 117 through 119 removed outlier: 6.777A pdb=" N ILE C 118 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 104 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL C 338 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE C 106 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N CYS C 312 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE C 339 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 362 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 243 through 245 removed outlier: 3.630A pdb=" N ILE C 193 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 192 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA C 196 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 145 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS C 169 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N TYR C 272 " --> pdb=" O HIS C 169 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL C 171 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 269 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 285 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR C 486 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=18, first strand: chain 'C' and resid 390 through 393 removed outlier: 6.496A pdb=" N LEU C 391 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=18 Processing sheet with id=19, first strand: chain 'C' and resid 454 through 457 removed outlier: 6.806A pdb=" N VAL C 470 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA C 512 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY C 472 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASP C 510 " --> pdb=" O GLY C 472 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU C 474 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 508 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N GLY C 509 " --> pdb=" O ARG C 525 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG C 525 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 511 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 529 through 532 Processing sheet with id=21, first strand: chain 'C' and resid 558 through 560 removed outlier: 3.935A pdb=" N LYS C 605 " --> pdb=" O VAL C 569 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1557 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: 2.74 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4953 1.34 - 1.46: 2656 1.46 - 1.57: 7898 1.57 - 1.69: 24 1.69 - 1.80: 123 Bond restraints: 15654 Sorted by residual: bond pdb=" O1A COA B 701 " pdb=" P1A COA B 701 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O1A COA A 701 " pdb=" P1A COA A 701 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" O1A COA C 701 " pdb=" P1A COA C 701 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" O8A COA A 701 " pdb=" P3B COA A 701 " ideal model delta sigma weight residual 1.514 1.608 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" O8A COA C 701 " pdb=" P3B COA C 701 " ideal model delta sigma weight residual 1.514 1.608 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 15649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 21207 3.03 - 6.07: 105 6.07 - 9.10: 15 9.10 - 12.13: 9 12.13 - 15.17: 9 Bond angle restraints: 21345 Sorted by residual: angle pdb=" C5B COA B 701 " pdb=" O5B COA B 701 " pdb=" P1A COA B 701 " ideal model delta sigma weight residual 120.98 105.81 15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C5B COA A 701 " pdb=" O5B COA A 701 " pdb=" P1A COA A 701 " ideal model delta sigma weight residual 120.98 105.82 15.16 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C5B COA C 701 " pdb=" O5B COA C 701 " pdb=" P1A COA C 701 " ideal model delta sigma weight residual 120.98 105.83 15.15 3.00e+00 1.11e-01 2.55e+01 angle pdb=" C3B COA B 701 " pdb=" C2B COA B 701 " pdb=" O2B COA B 701 " ideal model delta sigma weight residual 117.81 104.20 13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C3B COA C 701 " pdb=" C2B COA C 701 " pdb=" O2B COA C 701 " ideal model delta sigma weight residual 117.81 104.20 13.61 3.00e+00 1.11e-01 2.06e+01 ... (remaining 21340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 8057 16.98 - 33.96: 1005 33.96 - 50.95: 232 50.95 - 67.93: 60 67.93 - 84.91: 15 Dihedral angle restraints: 9369 sinusoidal: 3786 harmonic: 5583 Sorted by residual: dihedral pdb=" CA SER A 393 " pdb=" C SER A 393 " pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta harmonic sigma weight residual 180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER C 393 " pdb=" C SER C 393 " pdb=" N VAL C 394 " pdb=" CA VAL C 394 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER B 393 " pdb=" C SER B 393 " pdb=" N VAL B 394 " pdb=" CA VAL B 394 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 9366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2347 0.119 - 0.238: 20 0.238 - 0.357: 3 0.357 - 0.476: 0 0.476 - 0.594: 3 Chirality restraints: 2373 Sorted by residual: chirality pdb=" C2B COA C 701 " pdb=" C1B COA C 701 " pdb=" C3B COA C 701 " pdb=" O2B COA C 701 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" C2B COA A 701 " pdb=" C1B COA A 701 " pdb=" C3B COA A 701 " pdb=" O2B COA A 701 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" C2B COA B 701 " pdb=" C1B COA B 701 " pdb=" C3B COA B 701 " pdb=" O2B COA B 701 " both_signs ideal model delta sigma weight residual False -2.40 -3.00 0.59 2.00e-01 2.50e+01 8.76e+00 ... (remaining 2370 not shown) Planarity restraints: 2706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 263 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 264 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 264 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 264 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 263 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 264 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 263 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 264 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 264 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 264 " -0.027 5.00e-02 4.00e+02 ... (remaining 2703 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4240 2.80 - 3.32: 13854 3.32 - 3.85: 23991 3.85 - 4.37: 27890 4.37 - 4.90: 48820 Nonbonded interactions: 118795 Sorted by model distance: nonbonded pdb=" O2B COA C 701 " pdb=" O3B COA C 701 " model vdw 2.272 2.432 nonbonded pdb=" O2B COA A 701 " pdb=" O3B COA A 701 " model vdw 2.272 2.432 nonbonded pdb=" O2B COA B 701 " pdb=" O3B COA B 701 " model vdw 2.272 2.432 nonbonded pdb=" OE1 GLU B 396 " pdb=" O PRO B 397 " model vdw 2.409 3.040 nonbonded pdb=" OE1 GLU A 396 " pdb=" O PRO A 397 " model vdw 2.409 3.040 ... (remaining 118790 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.006 0.118 15654 Z= 0.264 Angle : 0.689 15.166 21345 Z= 0.315 Chirality : 0.052 0.594 2373 Planarity : 0.004 0.048 2706 Dihedral : 15.963 84.910 5799 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 2.18 % Allowed : 19.28 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1926 helix: 1.69 (0.21), residues: 588 sheet: -0.89 (0.29), residues: 318 loop : -1.39 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.013 0.002 TYR B 256 PHE 0.011 0.001 PHE A 403 TRP 0.011 0.001 TRP B 246 HIS 0.005 0.001 HIS B 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (15654) covalent geometry : angle 0.68875 / 0.31 (21345) hydrogen bonds : bond 0.24628 / 16.86 ( 537) hydrogen bonds : angle 8.06491 / 5.79 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 GLU cc_start: 0.7725 (mp0) cc_final: 0.7385 (mp0) REVERT: A 620 MET cc_start: 0.8588 (ptp) cc_final: 0.8330 (pmm) REVERT: A 635 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8152 (pp) REVERT: C 561 HIS cc_start: 0.2444 (OUTLIER) cc_final: 0.1782 (m170) outliers start: 35 outliers final: 11 residues processed: 166 average time/residue: 0.5163 time to fit residues: 94.8408 Evaluate side-chains 101 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 0.9980 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 531 ASN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 531 ASN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS C 531 ASN ** C 570 ASN ** 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 = 0.4226 r_free = 0.4226 target = 0.159008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.086565 restraints weight = 30819.690| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.41 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15654 Z= 0.157 Angle : 0.652 11.459 21345 Z= 0.332 Chirality : 0.048 0.161 2373 Planarity : 0.004 0.062 2706 Dihedral : 6.906 54.992 2331 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.92 % Allowed : 18.16 % Favored : 77.92 % 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: -0.34 (0.19), residues: 1926 helix: 1.79 (0.21), residues: 606 sheet: -0.67 (0.29), residues: 324 loop : -1.40 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 489 TYR 0.018 0.001 TYR A 579 PHE 0.020 0.001 PHE B 49 TRP 0.015 0.001 TRP C 246 HIS 0.009 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15654) covalent geometry : angle 0.65167 / 0.33 (21345) hydrogen bonds : bond 0.04949 / 3.35 ( 537) hydrogen bonds : angle 5.16876 / 3.71 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 98 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 GLU cc_start: 0.8109 (mp0) cc_final: 0.7640 (mp0) REVERT: A 620 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8322 (pmm) REVERT: B 347 ASP cc_start: 0.8648 (p0) cc_final: 0.8439 (p0) REVERT: C 53 MET cc_start: 0.9242 (tpp) cc_final: 0.8950 (tpp) outliers start: 63 outliers final: 19 residues processed: 146 average time/residue: 0.4410 time to fit residues: 72.9907 Evaluate side-chains 105 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 HIS A 95 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 429 HIS ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 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 = 0.4186 r_free = 0.4186 target = 0.155890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082222 restraints weight = 31289.127| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.55 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15654 Z= 0.244 Angle : 0.658 9.423 21345 Z= 0.334 Chirality : 0.048 0.154 2373 Planarity : 0.005 0.063 2706 Dihedral : 6.494 51.562 2314 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.54 % Allowed : 18.28 % Favored : 78.17 % 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 (0.19), residues: 1926 helix: 1.69 (0.21), residues: 606 sheet: -0.82 (0.29), residues: 321 loop : -1.46 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 489 TYR 0.018 0.002 TYR A 579 PHE 0.018 0.002 PHE C 253 TRP 0.020 0.002 TRP C 246 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 (15654) covalent geometry : angle 0.65756 / 0.33 (21345) hydrogen bonds : bond 0.05298 / 3.59 ( 537) hydrogen bonds : angle 4.84217 / 3.47 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 88 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9054 (mmt) REVERT: A 541 GLU cc_start: 0.8239 (mp0) cc_final: 0.7720 (mp0) REVERT: A 620 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8243 (pmm) REVERT: A 655 HIS cc_start: 0.9003 (m-70) cc_final: 0.8793 (m-70) REVERT: B 151 MET cc_start: 0.8052 (mmm) cc_final: 0.7783 (mmm) REVERT: B 364 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7447 (t80) REVERT: C 413 LYS cc_start: 0.9075 (mttt) cc_final: 0.8772 (mtmm) REVERT: C 422 TRP cc_start: 0.7524 (p-90) cc_final: 0.7277 (p-90) outliers start: 57 outliers final: 26 residues processed: 130 average time/residue: 0.4308 time to fit residues: 63.6626 Evaluate side-chains 110 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 55 optimal weight: 0.0570 chunk 175 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.156576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084068 restraints weight = 30533.447| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.63 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15654 Z= 0.158 Angle : 0.597 14.316 21345 Z= 0.298 Chirality : 0.046 0.251 2373 Planarity : 0.004 0.067 2706 Dihedral : 6.168 49.125 2314 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.17 % Allowed : 19.15 % Favored : 77.67 % 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: -0.38 (0.19), residues: 1926 helix: 1.78 (0.21), residues: 606 sheet: -0.75 (0.30), residues: 321 loop : -1.42 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 621 TYR 0.018 0.001 TYR A 579 PHE 0.013 0.001 PHE B 49 TRP 0.018 0.001 TRP B 521 HIS 0.005 0.001 HIS B 649 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15654) covalent geometry : angle 0.59735 / 0.30 (21345) hydrogen bonds : bond 0.03911 / 2.65 ( 537) hydrogen bonds : angle 4.51938 / 3.25 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 83 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.9052 (mmt) REVERT: A 541 GLU cc_start: 0.8256 (mp0) cc_final: 0.7717 (mp0) REVERT: A 620 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: A 655 HIS cc_start: 0.8894 (m-70) cc_final: 0.8662 (m-70) REVERT: B 151 MET cc_start: 0.8144 (mmm) cc_final: 0.7874 (mmm) REVERT: B 362 GLN cc_start: 0.8302 (mp10) cc_final: 0.7447 (mp10) outliers start: 51 outliers final: 26 residues processed: 123 average time/residue: 0.4749 time to fit residues: 65.4165 Evaluate side-chains 107 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 312 CYS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 185 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 189 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 HIS B 95 HIS B 135 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.156287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.083472 restraints weight = 30686.205| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.57 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15654 Z= 0.159 Angle : 0.592 14.679 21345 Z= 0.294 Chirality : 0.046 0.194 2373 Planarity : 0.004 0.065 2706 Dihedral : 6.004 46.446 2314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.86 % Allowed : 19.34 % Favored : 77.80 % 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: -0.28 (0.19), residues: 1926 helix: 1.71 (0.21), residues: 624 sheet: -0.58 (0.30), residues: 306 loop : -1.34 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.017 0.001 TYR A 579 PHE 0.012 0.001 PHE B 49 TRP 0.021 0.001 TRP B 521 HIS 0.005 0.001 HIS B 649 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (15654) covalent geometry : angle 0.59188 / 0.29 (21345) hydrogen bonds : bond 0.03948 / 2.66 ( 537) hydrogen bonds : angle 4.43854 / 3.19 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9207 (mmm) cc_final: 0.8874 (tpt) REVERT: A 238 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.9053 (mmt) REVERT: A 541 GLU cc_start: 0.8306 (mp0) cc_final: 0.7713 (mp0) REVERT: A 620 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8159 (pmm) REVERT: B 137 MET cc_start: 0.8169 (tmm) cc_final: 0.7799 (mtm) REVERT: B 362 GLN cc_start: 0.8456 (mp10) cc_final: 0.7267 (mp10) REVERT: B 542 ILE cc_start: 0.1206 (OUTLIER) cc_final: 0.0805 (tp) outliers start: 46 outliers final: 26 residues processed: 118 average time/residue: 0.4236 time to fit residues: 56.5366 Evaluate side-chains 106 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN C 535 HIS ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082186 restraints weight = 30461.354| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.27 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15654 Z= 0.246 Angle : 0.638 15.294 21345 Z= 0.320 Chirality : 0.048 0.153 2373 Planarity : 0.005 0.063 2706 Dihedral : 6.111 55.075 2314 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.61 % Allowed : 19.47 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.19), residues: 1926 helix: 1.81 (0.21), residues: 606 sheet: -0.69 (0.29), residues: 321 loop : -1.48 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 621 TYR 0.018 0.002 TYR A 579 PHE 0.012 0.001 PHE A 269 TRP 0.022 0.002 TRP B 521 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (15654) covalent geometry : angle 0.63810 / 0.32 (21345) hydrogen bonds : bond 0.04668 / 3.15 ( 537) hydrogen bonds : angle 4.57526 / 3.29 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 82 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8980 (mmt) REVERT: A 541 GLU cc_start: 0.8331 (mp0) cc_final: 0.7717 (mp0) REVERT: A 542 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9477 (mm) REVERT: A 573 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9011 (tp) REVERT: A 620 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8144 (pmm) REVERT: B 362 GLN cc_start: 0.8469 (mp10) cc_final: 0.7268 (mp10) REVERT: B 542 ILE cc_start: 0.1375 (OUTLIER) cc_final: 0.0953 (tp) REVERT: C 413 LYS cc_start: 0.9058 (mttt) cc_final: 0.8780 (mtmm) outliers start: 58 outliers final: 33 residues processed: 129 average time/residue: 0.4142 time to fit residues: 60.7314 Evaluate side-chains 118 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 80 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 191 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 182 optimal weight: 50.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 GLN B 423 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083498 restraints weight = 30335.963| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.37 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15654 Z= 0.151 Angle : 0.592 15.986 21345 Z= 0.293 Chirality : 0.046 0.300 2373 Planarity : 0.005 0.065 2706 Dihedral : 5.939 51.646 2314 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.67 % Allowed : 20.77 % Favored : 76.55 % 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: -0.26 (0.19), residues: 1926 helix: 1.93 (0.21), residues: 606 sheet: -0.66 (0.29), residues: 321 loop : -1.39 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.021 0.001 TYR C 35 PHE 0.014 0.001 PHE B 49 TRP 0.025 0.001 TRP B 521 HIS 0.007 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (15654) covalent geometry : angle 0.59210 / 0.29 (21345) hydrogen bonds : bond 0.03740 / 2.53 ( 537) hydrogen bonds : angle 4.37733 / 3.16 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9228 (mmm) cc_final: 0.8811 (tpt) REVERT: A 238 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.9039 (mmt) REVERT: A 541 GLU cc_start: 0.8336 (mp0) cc_final: 0.7744 (mp0) REVERT: A 573 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 620 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8116 (pmm) REVERT: A 658 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7018 (m-70) REVERT: B 137 MET cc_start: 0.8196 (tmm) cc_final: 0.7874 (mtp) REVERT: B 362 GLN cc_start: 0.8484 (mp10) cc_final: 0.7270 (mp10) REVERT: B 542 ILE cc_start: 0.1413 (OUTLIER) cc_final: 0.0999 (tp) REVERT: C 141 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: C 413 LYS cc_start: 0.9066 (mttt) cc_final: 0.8787 (mtmm) outliers start: 43 outliers final: 28 residues processed: 115 average time/residue: 0.4312 time to fit residues: 55.6641 Evaluate side-chains 115 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 182 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN C 378 ASN ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082653 restraints weight = 30605.165| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.35 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15654 Z= 0.200 Angle : 0.616 16.825 21345 Z= 0.304 Chirality : 0.047 0.297 2373 Planarity : 0.005 0.064 2706 Dihedral : 5.987 52.664 2314 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.86 % Allowed : 20.71 % Favored : 76.43 % 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: -0.26 (0.20), residues: 1926 helix: 1.93 (0.21), residues: 606 sheet: -0.67 (0.30), residues: 321 loop : -1.38 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 621 TYR 0.018 0.001 TYR A 579 PHE 0.014 0.001 PHE B 49 TRP 0.019 0.001 TRP B 521 HIS 0.010 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (15654) covalent geometry : angle 0.61619 / 0.30 (21345) hydrogen bonds : bond 0.04099 / 2.77 ( 537) hydrogen bonds : angle 4.42708 / 3.19 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 82 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.9021 (mmt) REVERT: A 541 GLU cc_start: 0.8338 (mp0) cc_final: 0.7741 (mp0) REVERT: A 573 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.8972 (tp) REVERT: A 620 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8086 (pmm) REVERT: A 658 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7084 (m-70) REVERT: B 362 GLN cc_start: 0.8478 (mp10) cc_final: 0.7241 (mp10) REVERT: B 542 ILE cc_start: 0.1420 (OUTLIER) cc_final: 0.1016 (tp) REVERT: C 141 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8481 (ttm) REVERT: C 413 LYS cc_start: 0.9054 (mttt) cc_final: 0.8781 (mtmm) outliers start: 46 outliers final: 32 residues processed: 119 average time/residue: 0.4751 time to fit residues: 63.2478 Evaluate side-chains 119 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 658 HIS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 0.3980 chunk 142 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 184 optimal weight: 50.0000 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 429 HIS ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 423 GLN ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.084855 restraints weight = 30304.732| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.61 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15654 Z= 0.103 Angle : 0.576 16.440 21345 Z= 0.282 Chirality : 0.045 0.259 2373 Planarity : 0.004 0.067 2706 Dihedral : 5.823 57.697 2314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.18 % Allowed : 21.64 % Favored : 76.18 % 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: -0.13 (0.19), residues: 1926 helix: 1.86 (0.21), residues: 624 sheet: -0.45 (0.30), residues: 306 loop : -1.28 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.018 0.001 TYR A 579 PHE 0.015 0.001 PHE B 49 TRP 0.018 0.001 TRP B 521 HIS 0.008 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (15654) covalent geometry : angle 0.57626 / 0.28 (21345) hydrogen bonds : bond 0.03173 / 2.17 ( 537) hydrogen bonds : angle 4.23940 / 3.07 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9185 (mmm) cc_final: 0.8833 (tpt) REVERT: A 541 GLU cc_start: 0.8370 (mp0) cc_final: 0.7718 (mp0) REVERT: A 620 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8053 (pmm) REVERT: A 652 HIS cc_start: 0.8787 (t70) cc_final: 0.8362 (m90) REVERT: B 137 MET cc_start: 0.8008 (tmm) cc_final: 0.7658 (mtm) REVERT: B 362 GLN cc_start: 0.8430 (mp10) cc_final: 0.7140 (mp10) REVERT: B 542 ILE cc_start: 0.1346 (OUTLIER) cc_final: 0.0956 (tp) REVERT: C 298 CYS cc_start: 0.9121 (m) cc_final: 0.8725 (m) REVERT: C 413 LYS cc_start: 0.9042 (mttt) cc_final: 0.8768 (mtmm) outliers start: 35 outliers final: 24 residues processed: 117 average time/residue: 0.4685 time to fit residues: 61.5910 Evaluate side-chains 109 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 130 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 0.0170 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 423 GLN C 113 ASN C 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.155918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088293 restraints weight = 30657.675| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.80 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15654 Z= 0.160 Angle : 0.618 16.297 21345 Z= 0.309 Chirality : 0.046 0.242 2373 Planarity : 0.005 0.064 2706 Dihedral : 5.766 57.311 2312 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.93 % Allowed : 21.89 % Favored : 76.18 % 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: -0.06 (0.20), residues: 1926 helix: 1.83 (0.21), residues: 624 sheet: -0.29 (0.32), residues: 285 loop : -1.21 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 621 TYR 0.100 0.002 TYR A 656 PHE 0.017 0.001 PHE B 49 TRP 0.016 0.001 TRP B 521 HIS 0.023 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (15654) covalent geometry : angle 0.61802 / 0.31 (21345) hydrogen bonds : bond 0.03807 / 2.62 ( 537) hydrogen bonds : angle 4.31641 / 3.13 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.9299 (mmm) cc_final: 0.8932 (tpt) REVERT: A 396 GLU cc_start: 0.7881 (tp30) cc_final: 0.7245 (tm-30) REVERT: A 541 GLU cc_start: 0.8580 (mp0) cc_final: 0.7935 (mp0) REVERT: A 620 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8152 (pmm) REVERT: B 137 MET cc_start: 0.8357 (tmm) cc_final: 0.7700 (mtp) REVERT: B 362 GLN cc_start: 0.8312 (mp10) cc_final: 0.7000 (mp10) REVERT: B 542 ILE cc_start: 0.1422 (OUTLIER) cc_final: 0.0949 (tp) REVERT: C 298 CYS cc_start: 0.9049 (m) cc_final: 0.8635 (m) REVERT: C 413 LYS cc_start: 0.9043 (mttt) cc_final: 0.8774 (mtmm) outliers start: 31 outliers final: 25 residues processed: 112 average time/residue: 0.4737 time to fit residues: 59.7183 Evaluate side-chains 110 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 423 GLN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain C residue 635 ILE Chi-restraints excluded: chain C residue 659 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 180 optimal weight: 50.0000 chunk 63 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 GLN C 113 ASN C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088159 restraints weight = 30369.347| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.79 r_work: 0.2816 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 15654 Z= 0.200 Angle : 0.806 59.186 21345 Z= 0.446 Chirality : 0.046 0.225 2373 Planarity : 0.005 0.064 2706 Dihedral : 5.766 57.220 2312 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.99 % Allowed : 21.95 % Favored : 76.06 % 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: -0.06 (0.19), residues: 1926 helix: 1.83 (0.21), residues: 624 sheet: -0.28 (0.32), residues: 285 loop : -1.21 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 621 TYR 0.056 0.001 TYR A 656 PHE 0.016 0.001 PHE B 49 TRP 0.014 0.001 TRP B 521 HIS 0.042 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (15654) covalent geometry : angle 0.80603 / 0.45 (21345) hydrogen bonds : bond 0.03861 / 2.66 ( 537) hydrogen bonds : angle 4.31916 / 3.13 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.72 seconds wall clock time: 66 minutes 27.57 seconds (3987.57 seconds total)