Starting phenix.real_space_refine on Sun Feb 8 09:59:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lpa_63269/02_2026/9lpa_63269.map" } resolution = 3.3 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= 0.004 sd= 0.100 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 360 5.49 5 S 88 5.16 5 C 26976 2.51 5 N 7408 2.21 5 O 9120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43952 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6122 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 23, 'TRANS': 719} Chain: "A" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3012 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 359} Chain: "C" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1173 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 21} Link IDs: {'rna2p': 6, 'rna3p': 48} Chain breaks: 3 Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, I, M, F, J, N, G, K, O, H, L, P Time building chain proxies: 9.25, per 1000 atoms: 0.21 Number of scatterers: 43952 At special positions: 0 Unit cell: (183.6, 214.8, 111.6, 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 88 16.00 P 360 15.00 O 9120 8.00 N 7408 7.00 C 26976 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: 4.04 Conformation dependent library (CDL) restraints added in 1.5 seconds 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8560 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 40 sheets defined 57.1% alpha, 11.0% beta 80 base pairs and 200 stacking pairs defined. Time for finding SS restraints: 5.71 Creating SS restraints... Processing helix chain 'B' and resid 35 through 51 removed outlier: 4.034A pdb=" N LEU B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.680A pdb=" N SER B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.544A pdb=" N ARG B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 170 through 178 removed outlier: 4.057A pdb=" N LYS B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 224 through 237 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 254 through 273 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.648A pdb=" N PHE B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.568A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 382 through 388 removed outlier: 3.846A pdb=" N LEU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 391 No H-bonds generated for 'chain 'B' and resid 389 through 391' Processing helix chain 'B' and resid 399 through 407 removed outlier: 3.748A pdb=" N LEU B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 removed outlier: 3.632A pdb=" N LEU B 414 " --> pdb=" O SER B 410 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.605A pdb=" N ASN B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.261A pdb=" N SER B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 467 through 478 Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.890A pdb=" N ASP B 482 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 483 " --> pdb=" O GLU B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 479 through 483' Processing helix chain 'B' and resid 488 through 501 Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 552 through 566 Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 591 through 599 Processing helix chain 'B' and resid 610 through 636 Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.618A pdb=" N ILE B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 669 through 682 Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 692 through 695 Processing helix chain 'B' and resid 696 through 713 removed outlier: 3.546A pdb=" N THR B 700 " --> pdb=" O GLY B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 727 through 743 removed outlier: 3.610A pdb=" N SER B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 17 removed outlier: 3.514A pdb=" N ILE A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.798A pdb=" N HIS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.836A pdb=" N TYR A 99 " --> pdb=" O PRO A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 168 through 192 removed outlier: 4.664A pdb=" N LYS A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.967A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.522A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.723A pdb=" N ILE A 304 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 344 removed outlier: 3.539A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 373 removed outlier: 3.636A pdb=" N ARG A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 4.058A pdb=" N LEU E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 85 removed outlier: 3.680A pdb=" N SER E 85 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 100 Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.544A pdb=" N ARG E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 170 through 178 removed outlier: 4.057A pdb=" N LYS E 174 " --> pdb=" O ASN E 170 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 200 Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 224 through 237 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 254 through 273 Processing helix chain 'E' and resid 292 through 310 removed outlier: 3.648A pdb=" N PHE E 310 " --> pdb=" O ILE E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 347 removed outlier: 3.569A pdb=" N LEU E 339 " --> pdb=" O SER E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 381 Processing helix chain 'E' and resid 382 through 388 removed outlier: 3.846A pdb=" N LEU E 388 " --> pdb=" O ASN E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 391 No H-bonds generated for 'chain 'E' and resid 389 through 391' Processing helix chain 'E' and resid 399 through 407 removed outlier: 3.748A pdb=" N LEU E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 removed outlier: 3.631A pdb=" N LEU E 414 " --> pdb=" O SER E 410 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 427 through 435 removed outlier: 3.605A pdb=" N ASN E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 4.260A pdb=" N SER E 439 " --> pdb=" O ASN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 454 No H-bonds generated for 'chain 'E' and resid 452 through 454' Processing helix chain 'E' and resid 467 through 478 Processing helix chain 'E' and resid 479 through 483 removed outlier: 3.890A pdb=" N ASP E 482 " --> pdb=" O LYS E 479 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR E 483 " --> pdb=" O GLU E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 483' Processing helix chain 'E' and resid 488 through 501 Processing helix chain 'E' and resid 519 through 532 Processing helix chain 'E' and resid 542 through 548 Processing helix chain 'E' and resid 552 through 566 Processing helix chain 'E' and resid 574 through 586 Processing helix chain 'E' and resid 591 through 599 Processing helix chain 'E' and resid 610 through 636 Processing helix chain 'E' and resid 638 through 651 removed outlier: 3.618A pdb=" N ILE E 642 " --> pdb=" O ASN E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 659 through 667 Processing helix chain 'E' and resid 669 through 682 Processing helix chain 'E' and resid 687 through 691 Processing helix chain 'E' and resid 692 through 695 Processing helix chain 'E' and resid 696 through 713 removed outlier: 3.546A pdb=" N THR E 700 " --> pdb=" O GLY E 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 727 Processing helix chain 'E' and resid 727 through 743 removed outlier: 3.610A pdb=" N SER E 732 " --> pdb=" O PRO E 728 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 4.058A pdb=" N LEU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 85 removed outlier: 3.680A pdb=" N SER I 85 " --> pdb=" O LYS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 100 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 143 through 154 removed outlier: 3.544A pdb=" N ARG I 147 " --> pdb=" O ASP I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 164 No H-bonds generated for 'chain 'I' and resid 162 through 164' Processing helix chain 'I' and resid 170 through 178 removed outlier: 4.057A pdb=" N LYS I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU I 175 " --> pdb=" O PRO I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 200 Processing helix chain 'I' and resid 205 through 218 Processing helix chain 'I' and resid 224 through 237 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 254 through 273 Processing helix chain 'I' and resid 292 through 310 removed outlier: 3.647A pdb=" N PHE I 310 " --> pdb=" O ILE I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 347 removed outlier: 3.568A pdb=" N LEU I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 381 Processing helix chain 'I' and resid 382 through 388 removed outlier: 3.847A pdb=" N LEU I 388 " --> pdb=" O ASN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 391 No H-bonds generated for 'chain 'I' and resid 389 through 391' Processing helix chain 'I' and resid 399 through 407 removed outlier: 3.748A pdb=" N LEU I 403 " --> pdb=" O GLY I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 415 removed outlier: 3.631A pdb=" N LEU I 414 " --> pdb=" O SER I 410 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 415 " --> pdb=" O LEU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 421 Processing helix chain 'I' and resid 427 through 435 removed outlier: 3.605A pdb=" N ASN I 435 " --> pdb=" O LEU I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 440 removed outlier: 4.260A pdb=" N SER I 439 " --> pdb=" O ASN I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 454 No H-bonds generated for 'chain 'I' and resid 452 through 454' Processing helix chain 'I' and resid 467 through 478 Processing helix chain 'I' and resid 479 through 483 removed outlier: 3.890A pdb=" N ASP I 482 " --> pdb=" O LYS I 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR I 483 " --> pdb=" O GLU I 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 479 through 483' Processing helix chain 'I' and resid 488 through 501 Processing helix chain 'I' and resid 519 through 532 Processing helix chain 'I' and resid 542 through 548 Processing helix chain 'I' and resid 552 through 566 Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 591 through 599 Processing helix chain 'I' and resid 610 through 636 Processing helix chain 'I' and resid 638 through 651 removed outlier: 3.618A pdb=" N ILE I 642 " --> pdb=" O ASN I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 659 through 667 Processing helix chain 'I' and resid 669 through 682 Processing helix chain 'I' and resid 687 through 691 Processing helix chain 'I' and resid 692 through 695 Processing helix chain 'I' and resid 696 through 713 removed outlier: 3.546A pdb=" N THR I 700 " --> pdb=" O GLY I 696 " (cutoff:3.500A) Processing helix chain 'I' and resid 715 through 727 Processing helix chain 'I' and resid 727 through 743 removed outlier: 3.610A pdb=" N SER I 732 " --> pdb=" O PRO I 728 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 51 removed outlier: 4.058A pdb=" N LEU M 40 " --> pdb=" O LYS M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 85 removed outlier: 3.680A pdb=" N SER M 85 " --> pdb=" O LYS M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 100 Processing helix chain 'M' and resid 109 through 119 Processing helix chain 'M' and resid 143 through 154 removed outlier: 3.545A pdb=" N ARG M 147 " --> pdb=" O ASP M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 164 No H-bonds generated for 'chain 'M' and resid 162 through 164' Processing helix chain 'M' and resid 170 through 178 removed outlier: 4.057A pdb=" N LYS M 174 " --> pdb=" O ASN M 170 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 175 " --> pdb=" O PRO M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'M' and resid 205 through 218 Processing helix chain 'M' and resid 224 through 237 Processing helix chain 'M' and resid 248 through 252 Processing helix chain 'M' and resid 254 through 273 Processing helix chain 'M' and resid 292 through 310 removed outlier: 3.648A pdb=" N PHE M 310 " --> pdb=" O ILE M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 347 removed outlier: 3.568A pdb=" N LEU M 339 " --> pdb=" O SER M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 381 Processing helix chain 'M' and resid 382 through 388 removed outlier: 3.847A pdb=" N LEU M 388 " --> pdb=" O ASN M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 391 No H-bonds generated for 'chain 'M' and resid 389 through 391' Processing helix chain 'M' and resid 399 through 407 removed outlier: 3.748A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 415 removed outlier: 3.631A pdb=" N LEU M 414 " --> pdb=" O SER M 410 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR M 415 " --> pdb=" O LEU M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 421 Processing helix chain 'M' and resid 427 through 435 removed outlier: 3.606A pdb=" N ASN M 435 " --> pdb=" O LEU M 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 435 through 440 removed outlier: 4.261A pdb=" N SER M 439 " --> pdb=" O ASN M 435 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 467 through 478 Processing helix chain 'M' and resid 479 through 483 removed outlier: 3.891A pdb=" N ASP M 482 " --> pdb=" O LYS M 479 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR M 483 " --> pdb=" O GLU M 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 479 through 483' Processing helix chain 'M' and resid 488 through 501 Processing helix chain 'M' and resid 519 through 532 Processing helix chain 'M' and resid 542 through 548 Processing helix chain 'M' and resid 552 through 566 Processing helix chain 'M' and resid 574 through 586 Processing helix chain 'M' and resid 591 through 599 Processing helix chain 'M' and resid 610 through 636 Processing helix chain 'M' and resid 638 through 651 removed outlier: 3.619A pdb=" N ILE M 642 " --> pdb=" O ASN M 638 " (cutoff:3.500A) Processing helix chain 'M' and resid 659 through 667 Processing helix chain 'M' and resid 669 through 682 Processing helix chain 'M' and resid 687 through 691 Processing helix chain 'M' and resid 692 through 695 Processing helix chain 'M' and resid 696 through 713 removed outlier: 3.545A pdb=" N THR M 700 " --> pdb=" O GLY M 696 " (cutoff:3.500A) Processing helix chain 'M' and resid 715 through 727 Processing helix chain 'M' and resid 727 through 743 removed outlier: 3.610A pdb=" N SER M 732 " --> pdb=" O PRO M 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 17 removed outlier: 3.514A pdb=" N ILE F 17 " --> pdb=" O PHE F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 58 through 71 removed outlier: 3.797A pdb=" N HIS F 62 " --> pdb=" O SER F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.836A pdb=" N TYR F 99 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 168 through 192 removed outlier: 4.665A pdb=" N LYS F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET F 180 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 227 removed outlier: 3.967A pdb=" N ILE F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.522A pdb=" N LEU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL F 274 " --> pdb=" O LYS F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.723A pdb=" N ILE F 304 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 344 removed outlier: 3.539A pdb=" N LYS F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 373 removed outlier: 3.636A pdb=" N ARG F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 17 removed outlier: 3.515A pdb=" N ILE J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 29 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 58 through 71 removed outlier: 3.798A pdb=" N HIS J 62 " --> pdb=" O SER J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 96 through 100 removed outlier: 3.836A pdb=" N TYR J 99 " --> pdb=" O PRO J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 125 Processing helix chain 'J' and resid 126 through 128 No H-bonds generated for 'chain 'J' and resid 126 through 128' Processing helix chain 'J' and resid 140 through 149 Processing helix chain 'J' and resid 168 through 192 removed outlier: 4.664A pdb=" N LYS J 179 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET J 180 " --> pdb=" O VAL J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 227 removed outlier: 3.966A pdb=" N ILE J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 283 removed outlier: 3.522A pdb=" N LEU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR J 273 " --> pdb=" O SER J 269 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL J 274 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 294 Processing helix chain 'J' and resid 300 through 304 removed outlier: 3.723A pdb=" N ILE J 304 " --> pdb=" O GLU J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 344 removed outlier: 3.539A pdb=" N LYS J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 373 removed outlier: 3.636A pdb=" N ARG J 373 " --> pdb=" O LYS J 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 17 removed outlier: 3.515A pdb=" N ILE N 17 " --> pdb=" O PHE N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 29 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 58 through 71 removed outlier: 3.797A pdb=" N HIS N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 95 Processing helix chain 'N' and resid 96 through 100 removed outlier: 3.835A pdb=" N TYR N 99 " --> pdb=" O PRO N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 125 Processing helix chain 'N' and resid 126 through 128 No H-bonds generated for 'chain 'N' and resid 126 through 128' Processing helix chain 'N' and resid 140 through 149 Processing helix chain 'N' and resid 168 through 192 removed outlier: 4.663A pdb=" N LYS N 179 " --> pdb=" O ILE N 175 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET N 180 " --> pdb=" O VAL N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 227 removed outlier: 3.967A pdb=" N ILE N 219 " --> pdb=" O SER N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 283 removed outlier: 3.522A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR N 273 " --> pdb=" O SER N 269 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL N 274 " --> pdb=" O LYS N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 294 Processing helix chain 'N' and resid 300 through 304 removed outlier: 3.724A pdb=" N ILE N 304 " --> pdb=" O GLU N 301 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 344 removed outlier: 3.540A pdb=" N LYS N 315 " --> pdb=" O ASP N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 373 removed outlier: 3.636A pdb=" N ARG N 373 " --> pdb=" O LYS N 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.976A pdb=" N ASP B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 73 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 6 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 8 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU B 69 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN B 10 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 67 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.193A pdb=" N VAL B 282 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N SER B 332 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 284 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 352 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 422 through 425 removed outlier: 6.387A pdb=" N ILE B 394 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 448 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 396 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP B 450 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR B 537 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE B 447 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET B 539 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LYS B 449 " --> pdb=" O MET B 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AA5, first strand: chain 'B' and resid 568 through 570 Processing sheet with id=AA6, first strand: chain 'A' and resid 41 through 46 Processing sheet with id=AA7, first strand: chain 'A' and resid 194 through 198 Processing sheet with id=AA8, first strand: chain 'A' and resid 132 through 134 removed outlier: 3.663A pdb=" N GLN A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AB2, first strand: chain 'E' and resid 14 through 20 removed outlier: 6.976A pdb=" N ASP E 15 " --> pdb=" O ASN E 10 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR E 73 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 6 " --> pdb=" O THR E 71 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR E 71 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL E 8 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU E 69 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN E 10 " --> pdb=" O VAL E 67 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 67 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.193A pdb=" N VAL E 282 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER E 332 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE E 284 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL E 352 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 422 through 425 removed outlier: 6.386A pdb=" N ILE E 394 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE E 448 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE E 396 " --> pdb=" O ILE E 448 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP E 450 " --> pdb=" O PHE E 396 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR E 537 " --> pdb=" O PHE E 445 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE E 447 " --> pdb=" O TYR E 537 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET E 539 " --> pdb=" O ILE E 447 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS E 449 " --> pdb=" O MET E 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 508 through 509 Processing sheet with id=AB6, first strand: chain 'E' and resid 568 through 570 Processing sheet with id=AB7, first strand: chain 'I' and resid 14 through 20 removed outlier: 6.977A pdb=" N ASP I 15 " --> pdb=" O ASN I 10 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR I 73 " --> pdb=" O GLU I 4 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE I 6 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR I 71 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL I 8 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU I 69 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN I 10 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL I 67 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 156 through 160 removed outlier: 6.192A pdb=" N VAL I 282 " --> pdb=" O PHE I 330 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER I 332 " --> pdb=" O VAL I 282 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE I 284 " --> pdb=" O SER I 332 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL I 352 " --> pdb=" O ILE I 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 422 through 425 removed outlier: 6.387A pdb=" N ILE I 394 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE I 448 " --> pdb=" O ILE I 394 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE I 396 " --> pdb=" O ILE I 448 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP I 450 " --> pdb=" O PHE I 396 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR I 537 " --> pdb=" O PHE I 445 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE I 447 " --> pdb=" O TYR I 537 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET I 539 " --> pdb=" O ILE I 447 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS I 449 " --> pdb=" O MET I 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 508 through 509 Processing sheet with id=AC2, first strand: chain 'I' and resid 568 through 570 Processing sheet with id=AC3, first strand: chain 'M' and resid 14 through 20 removed outlier: 6.976A pdb=" N ASP M 15 " --> pdb=" O ASN M 10 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR M 73 " --> pdb=" O GLU M 4 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE M 6 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR M 71 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL M 8 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU M 69 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN M 10 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL M 67 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 156 through 160 removed outlier: 6.192A pdb=" N VAL M 282 " --> pdb=" O PHE M 330 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N SER M 332 " --> pdb=" O VAL M 282 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE M 284 " --> pdb=" O SER M 332 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL M 352 " --> pdb=" O ILE M 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 422 through 425 removed outlier: 6.387A pdb=" N ILE M 394 " --> pdb=" O VAL M 446 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE M 448 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE M 396 " --> pdb=" O ILE M 448 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N ASP M 450 " --> pdb=" O PHE M 396 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N TYR M 537 " --> pdb=" O PHE M 445 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE M 447 " --> pdb=" O TYR M 537 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET M 539 " --> pdb=" O ILE M 447 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS M 449 " --> pdb=" O MET M 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 508 through 509 Processing sheet with id=AC7, first strand: chain 'M' and resid 568 through 570 Processing sheet with id=AC8, first strand: chain 'F' and resid 41 through 46 Processing sheet with id=AC9, first strand: chain 'F' and resid 194 through 198 Processing sheet with id=AD1, first strand: chain 'F' and resid 132 through 134 removed outlier: 3.662A pdb=" N GLN F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 150 through 151 Processing sheet with id=AD3, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AD4, first strand: chain 'J' and resid 41 through 46 Processing sheet with id=AD5, first strand: chain 'J' and resid 194 through 198 Processing sheet with id=AD6, first strand: chain 'J' and resid 132 through 134 removed outlier: 3.663A pdb=" N GLN J 138 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 150 through 151 Processing sheet with id=AD8, first strand: chain 'J' and resid 244 through 247 Processing sheet with id=AD9, first strand: chain 'N' and resid 41 through 46 Processing sheet with id=AE1, first strand: chain 'N' and resid 194 through 198 Processing sheet with id=AE2, first strand: chain 'N' and resid 132 through 134 removed outlier: 3.663A pdb=" N GLN N 138 " --> pdb=" O ILE N 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 150 through 151 Processing sheet with id=AE4, first strand: chain 'N' and resid 244 through 247 1868 hydrogen bonds defined for protein. 5376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 192 hydrogen bonds 360 hydrogen bond angles 0 basepair planarities 80 basepair parallelities 200 stacking parallelities Total time for adding SS restraints: 9.92 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6412 1.31 - 1.44: 14138 1.44 - 1.56: 24170 1.56 - 1.69: 692 1.69 - 1.81: 148 Bond restraints: 45560 Sorted by residual: bond pdb=" CA SER I 253 " pdb=" CB SER I 253 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.44e-02 4.82e+03 2.18e+01 bond pdb=" CA SER E 253 " pdb=" CB SER E 253 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.44e-02 4.82e+03 2.17e+01 bond pdb=" CA SER B 253 " pdb=" CB SER B 253 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.44e-02 4.82e+03 2.17e+01 bond pdb=" CA SER M 253 " pdb=" CB SER M 253 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.44e-02 4.82e+03 2.17e+01 bond pdb=" CA SER J 246 " pdb=" CB SER J 246 " ideal model delta sigma weight residual 1.530 1.461 0.070 1.50e-02 4.44e+03 2.16e+01 ... (remaining 45555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 62101 2.85 - 5.70: 859 5.70 - 8.55: 56 8.55 - 11.40: 4 11.40 - 14.25: 4 Bond angle restraints: 63024 Sorted by residual: angle pdb=" PB ATP I 801 " pdb=" O3B ATP I 801 " pdb=" PG ATP I 801 " ideal model delta sigma weight residual 139.87 125.62 14.25 1.00e+00 1.00e+00 2.03e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 125.65 14.22 1.00e+00 1.00e+00 2.02e+02 angle pdb=" PB ATP M 801 " pdb=" O3B ATP M 801 " pdb=" PG ATP M 801 " ideal model delta sigma weight residual 139.87 125.66 14.21 1.00e+00 1.00e+00 2.02e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 125.67 14.20 1.00e+00 1.00e+00 2.02e+02 angle pdb=" PA ATP E 801 " pdb=" O3A ATP E 801 " pdb=" PB ATP E 801 " ideal model delta sigma weight residual 136.83 129.56 7.27 1.00e+00 1.00e+00 5.28e+01 ... (remaining 63019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 25628 35.44 - 70.88: 1804 70.88 - 106.31: 128 106.31 - 141.75: 12 141.75 - 177.19: 20 Dihedral angle restraints: 27592 sinusoidal: 14360 harmonic: 13232 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 37.41 162.59 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U O 21 " pdb=" C1' U O 21 " pdb=" N1 U O 21 " pdb=" C2 U O 21 " ideal model delta sinusoidal sigma weight residual 200.00 37.47 162.53 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U G 21 " pdb=" C1' U G 21 " pdb=" N1 U G 21 " pdb=" C2 U G 21 " ideal model delta sinusoidal sigma weight residual 200.00 37.47 162.53 1 1.50e+01 4.44e-03 8.34e+01 ... (remaining 27589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 6118 0.065 - 0.129: 847 0.129 - 0.194: 185 0.194 - 0.258: 54 0.258 - 0.323: 20 Chirality restraints: 7224 Sorted by residual: chirality pdb=" CA ILE F 264 " pdb=" N ILE F 264 " pdb=" C ILE F 264 " pdb=" CB ILE F 264 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ILE A 264 " pdb=" N ILE A 264 " pdb=" C ILE A 264 " pdb=" CB ILE A 264 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ILE N 264 " pdb=" N ILE N 264 " pdb=" C ILE N 264 " pdb=" CB ILE N 264 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 7221 not shown) Planarity restraints: 6680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 330 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C ARG A 330 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG A 330 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 331 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 330 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C ARG N 330 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG N 330 " -0.016 2.00e-02 2.50e+03 pdb=" N SER N 331 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 330 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ARG F 330 " -0.042 2.00e-02 2.50e+03 pdb=" O ARG F 330 " 0.016 2.00e-02 2.50e+03 pdb=" N SER F 331 " 0.014 2.00e-02 2.50e+03 ... (remaining 6677 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4923 2.74 - 3.28: 42033 3.28 - 3.82: 76748 3.82 - 4.36: 89753 4.36 - 4.90: 149260 Nonbonded interactions: 362717 Sorted by model distance: nonbonded pdb=" O PHE F 166 " pdb=" N THR F 168 " model vdw 2.204 3.120 nonbonded pdb=" O PHE J 166 " pdb=" N THR J 168 " model vdw 2.204 3.120 nonbonded pdb=" O PHE A 166 " pdb=" N THR A 168 " model vdw 2.204 3.120 nonbonded pdb=" O PHE N 166 " pdb=" N THR N 168 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN E 65 " pdb=" OG SER F 79 " model vdw 2.231 3.040 ... (remaining 362712 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 42.930 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 45560 Z= 0.303 Angle : 0.755 14.245 63024 Z= 0.482 Chirality : 0.055 0.323 7224 Planarity : 0.004 0.048 6680 Dihedral : 21.720 177.190 19032 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.89 % Favored : 96.75 % Rotamer: Outliers : 1.38 % Allowed : 22.64 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.13), residues: 4436 helix: 1.52 (0.11), residues: 2232 sheet: 0.29 (0.21), residues: 620 loop : -0.39 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 630 TYR 0.029 0.002 TYR F 93 PHE 0.031 0.002 PHE E 624 TRP 0.005 0.001 TRP B 139 HIS 0.006 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00540 (45560) covalent geometry : angle 0.75537 (63024) hydrogen bonds : bond 0.13372 ( 2060) hydrogen bonds : angle 5.44295 ( 5736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 358 time to evaluate : 1.587 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: symmetry clash revert: symmetry clash REVERT: B 33 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8782 (m-40) REVERT: B 582 MET cc_start: 0.6207 (mmt) cc_final: 0.5194 (mmm) REVERT: A 251 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9157 (m) REVERT: E 33 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8789 (m-40) REVERT: E 582 MET cc_start: 0.6212 (mmt) cc_final: 0.5204 (mmm) REVERT: I 33 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8776 (m-40) REVERT: I 582 MET cc_start: 0.6339 (mmt) cc_final: 0.5301 (mmm) REVERT: M 33 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8771 (m-40) REVERT: M 582 MET cc_start: 0.6130 (mmt) cc_final: 0.5109 (mmm) REVERT: J 251 VAL cc_start: 0.9400 (OUTLIER) cc_final: 0.9155 (m) REVERT: N 251 VAL cc_start: 0.9397 (OUTLIER) cc_final: 0.9147 (m) outliers start: 57 outliers final: 22 residues processed: 403 average time/residue: 0.2819 time to fit residues: 182.3299 Evaluate side-chains 361 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 540 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 246 SER Chi-restraints excluded: chain J residue 251 VAL Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 253 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 470 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN B 252 GLN B 558 ASN E 183 ASN E 252 GLN E 558 ASN I 183 ASN I 189 HIS I 252 GLN I 558 ASN M 183 ASN M 252 GLN M 558 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103217 restraints weight = 66077.588| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.08 r_work: 0.3188 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45560 Z= 0.135 Angle : 0.544 5.823 63024 Z= 0.295 Chirality : 0.041 0.208 7224 Planarity : 0.003 0.047 6680 Dihedral : 21.774 177.185 9841 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.10 % Favored : 97.63 % Rotamer: Outliers : 3.38 % Allowed : 19.26 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.13), residues: 4436 helix: 1.75 (0.11), residues: 2244 sheet: 0.33 (0.21), residues: 608 loop : -0.42 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 20 TYR 0.014 0.001 TYR I 331 PHE 0.016 0.001 PHE I 250 TRP 0.006 0.001 TRP I 559 HIS 0.005 0.001 HIS I 189 Details of bonding type rmsd covalent geometry : bond 0.00302 (45560) covalent geometry : angle 0.54351 (63024) hydrogen bonds : bond 0.03944 ( 2060) hydrogen bonds : angle 4.17576 ( 5736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 397 time to evaluate : 1.562 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ASP cc_start: 0.8276 (t0) cc_final: 0.7599 (m-30) REVERT: B 174 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8532 (mmmm) REVERT: B 198 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 479 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7515 (tppt) REVERT: B 482 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: B 497 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 509 MET cc_start: 0.7237 (ptm) cc_final: 0.6644 (ptm) REVERT: B 582 MET cc_start: 0.5995 (mmt) cc_final: 0.5481 (mmm) REVERT: A 158 LYS cc_start: 0.6586 (pttt) cc_final: 0.6346 (pttt) REVERT: E 174 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8534 (mmmm) REVERT: E 198 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: E 479 LYS cc_start: 0.8009 (mtpt) cc_final: 0.7519 (tppt) REVERT: E 482 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: E 497 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8207 (mp) REVERT: E 509 MET cc_start: 0.7262 (ptm) cc_final: 0.6713 (ptm) REVERT: E 582 MET cc_start: 0.5995 (mmt) cc_final: 0.5476 (mmm) REVERT: I 198 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: I 479 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7490 (tppt) REVERT: I 482 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: I 497 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8257 (mp) REVERT: I 582 MET cc_start: 0.6034 (mmt) cc_final: 0.5537 (mmm) REVERT: M 143 ASP cc_start: 0.8283 (t0) cc_final: 0.7607 (m-30) REVERT: M 174 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8544 (mmmm) REVERT: M 198 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: M 479 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7507 (tppt) REVERT: M 482 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: M 497 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8243 (mp) REVERT: M 509 MET cc_start: 0.7244 (ptm) cc_final: 0.6652 (ptm) REVERT: M 582 MET cc_start: 0.6051 (mmt) cc_final: 0.5526 (mmm) REVERT: F 158 LYS cc_start: 0.6564 (pttt) cc_final: 0.6317 (pttt) REVERT: J 158 LYS cc_start: 0.6575 (pttt) cc_final: 0.6329 (pttt) REVERT: N 158 LYS cc_start: 0.6561 (pttt) cc_final: 0.5207 (mttm) outliers start: 140 outliers final: 71 residues processed: 512 average time/residue: 0.2719 time to fit residues: 228.3701 Evaluate side-chains 431 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 345 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 497 LEU Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 285 ASP Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 497 LEU Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 157 ASP Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 157 ASP Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 253 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 237 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 385 optimal weight: 0.0670 chunk 202 optimal weight: 1.9990 chunk 470 optimal weight: 10.0000 chunk 436 optimal weight: 3.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 HIS E 354 HIS I 354 HIS I 574 ASN M 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101321 restraints weight = 65529.050| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.08 r_work: 0.3133 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45560 Z= 0.174 Angle : 0.546 7.856 63024 Z= 0.296 Chirality : 0.041 0.216 7224 Planarity : 0.003 0.046 6680 Dihedral : 21.551 177.404 9812 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.48 % Favored : 97.25 % Rotamer: Outliers : 3.33 % Allowed : 20.80 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.13), residues: 4436 helix: 1.70 (0.11), residues: 2272 sheet: 0.20 (0.21), residues: 604 loop : -0.42 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 20 TYR 0.014 0.001 TYR I 331 PHE 0.025 0.001 PHE I 624 TRP 0.005 0.001 TRP E 173 HIS 0.005 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00410 (45560) covalent geometry : angle 0.54634 (63024) hydrogen bonds : bond 0.03990 ( 2060) hydrogen bonds : angle 4.06838 ( 5736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 345 time to evaluate : 1.439 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 ASP cc_start: 0.8318 (t0) cc_final: 0.7610 (m-30) REVERT: B 174 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8499 (mmmm) REVERT: B 198 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: B 476 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8157 (mt-10) REVERT: B 479 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7475 (tppt) REVERT: B 509 MET cc_start: 0.7269 (ptm) cc_final: 0.6772 (ptm) REVERT: A 158 LYS cc_start: 0.6705 (pttt) cc_final: 0.5982 (mttm) REVERT: A 229 MET cc_start: 0.9160 (mtp) cc_final: 0.8832 (mtm) REVERT: E 174 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8496 (mmmm) REVERT: E 198 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: E 476 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8170 (mt-10) REVERT: E 479 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7497 (tppt) REVERT: E 509 MET cc_start: 0.7279 (ptm) cc_final: 0.6811 (ptm) REVERT: E 582 MET cc_start: 0.5945 (mmt) cc_final: 0.5289 (mmm) REVERT: I 198 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: I 476 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8155 (mt-10) REVERT: I 479 LYS cc_start: 0.7925 (mtpt) cc_final: 0.7408 (tppt) REVERT: I 544 GLU cc_start: 0.8137 (mp0) cc_final: 0.7875 (mt-10) REVERT: M 143 ASP cc_start: 0.8330 (t0) cc_final: 0.7623 (m-30) REVERT: M 174 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8526 (mmmm) REVERT: M 198 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: M 476 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8151 (mt-10) REVERT: M 479 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7484 (tppt) REVERT: M 509 MET cc_start: 0.7285 (ptm) cc_final: 0.6798 (ptm) REVERT: M 582 MET cc_start: 0.6020 (mmt) cc_final: 0.5354 (mmm) REVERT: F 158 LYS cc_start: 0.6660 (pttt) cc_final: 0.5978 (mttm) REVERT: F 229 MET cc_start: 0.9163 (mtp) cc_final: 0.8835 (mtm) REVERT: J 158 LYS cc_start: 0.6693 (pttt) cc_final: 0.6001 (mttm) REVERT: J 229 MET cc_start: 0.9160 (mtp) cc_final: 0.8823 (mtm) REVERT: N 158 LYS cc_start: 0.6667 (pttt) cc_final: 0.5981 (mttm) REVERT: N 229 MET cc_start: 0.9162 (mtp) cc_final: 0.8834 (mtm) outliers start: 138 outliers final: 85 residues processed: 462 average time/residue: 0.2675 time to fit residues: 203.0781 Evaluate side-chains 406 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 314 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 676 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 676 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 377 optimal weight: 10.0000 chunk 351 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 411 optimal weight: 3.9990 chunk 413 optimal weight: 1.9990 chunk 459 optimal weight: 7.9990 chunk 449 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 558 ASN A 26 ASN E 121 ASN E 558 ASN I 121 ASN I 292 HIS I 558 ASN M 121 ASN M 558 ASN F 26 ASN J 26 ASN N 26 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097700 restraints weight = 65870.897| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.04 r_work: 0.3080 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 45560 Z= 0.274 Angle : 0.615 7.187 63024 Z= 0.332 Chirality : 0.045 0.218 7224 Planarity : 0.004 0.045 6680 Dihedral : 21.534 176.254 9792 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.80 % Favored : 96.91 % Rotamer: Outliers : 4.44 % Allowed : 19.91 % Favored : 75.65 % 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: 0.80 (0.13), residues: 4436 helix: 1.46 (0.11), residues: 2284 sheet: -0.10 (0.21), residues: 608 loop : -0.52 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 492 TYR 0.023 0.002 TYR E 457 PHE 0.022 0.002 PHE I 624 TRP 0.006 0.002 TRP I 559 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00652 (45560) covalent geometry : angle 0.61456 (63024) hydrogen bonds : bond 0.04478 ( 2060) hydrogen bonds : angle 4.24449 ( 5736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 321 time to evaluate : 1.578 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: symmetry clash REVERT: B 33 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8819 (m-40) REVERT: B 143 ASP cc_start: 0.8454 (t0) cc_final: 0.7913 (m-30) REVERT: B 174 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8555 (mmmm) REVERT: B 198 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: B 482 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: B 509 MET cc_start: 0.7296 (ptm) cc_final: 0.6845 (ptm) REVERT: A 158 LYS cc_start: 0.6764 (pttt) cc_final: 0.6008 (mttm) REVERT: A 166 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7720 (t80) REVERT: E 33 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.8887 (m-40) REVERT: E 174 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8581 (mmmm) REVERT: E 198 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 482 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: I 33 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8850 (m-40) REVERT: I 198 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: I 482 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: M 33 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8838 (m-40) REVERT: M 143 ASP cc_start: 0.8524 (t0) cc_final: 0.8006 (m-30) REVERT: M 174 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8525 (mmmm) REVERT: M 198 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: M 482 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: M 509 MET cc_start: 0.7265 (ptm) cc_final: 0.6789 (ptm) REVERT: F 158 LYS cc_start: 0.6629 (pttt) cc_final: 0.5858 (mttm) REVERT: F 166 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7650 (t80) REVERT: J 158 LYS cc_start: 0.6768 (pttt) cc_final: 0.6010 (mttm) REVERT: J 166 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7659 (t80) REVERT: N 158 LYS cc_start: 0.6683 (pttt) cc_final: 0.5922 (mttm) REVERT: N 166 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7641 (t80) outliers start: 184 outliers final: 95 residues processed: 458 average time/residue: 0.2615 time to fit residues: 198.4514 Evaluate side-chains 411 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 297 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 52 ASN Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 371 THR Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 308 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100790 restraints weight = 65626.415| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.06 r_work: 0.3127 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45560 Z= 0.146 Angle : 0.537 8.270 63024 Z= 0.292 Chirality : 0.041 0.215 7224 Planarity : 0.003 0.047 6680 Dihedral : 21.350 176.248 9792 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.39 % Favored : 97.27 % Rotamer: Outliers : 3.31 % Allowed : 21.02 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.13), residues: 4436 helix: 1.68 (0.11), residues: 2264 sheet: -0.10 (0.21), residues: 604 loop : -0.41 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 630 TYR 0.014 0.001 TYR M 331 PHE 0.018 0.001 PHE I 624 TRP 0.010 0.001 TRP I 559 HIS 0.004 0.001 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00335 (45560) covalent geometry : angle 0.53678 (63024) hydrogen bonds : bond 0.03734 ( 2060) hydrogen bonds : angle 4.08367 ( 5736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 340 time to evaluate : 1.666 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: symmetry clash revert: symmetry clash REVERT: B 33 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8757 (m-40) REVERT: B 121 ASN cc_start: 0.6287 (OUTLIER) cc_final: 0.6053 (m-40) REVERT: B 143 ASP cc_start: 0.8352 (t0) cc_final: 0.7765 (m-30) REVERT: B 174 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8501 (mmmm) REVERT: B 181 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8516 (p) REVERT: B 198 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: B 374 ASP cc_start: 0.8207 (t0) cc_final: 0.7820 (t0) REVERT: B 476 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8197 (mt-10) REVERT: B 479 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7445 (tppt) REVERT: B 482 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7772 (m-30) REVERT: B 509 MET cc_start: 0.7240 (ptm) cc_final: 0.6777 (ptm) REVERT: B 544 GLU cc_start: 0.8236 (mp0) cc_final: 0.7814 (mt-10) REVERT: A 6 MET cc_start: 0.6979 (ppp) cc_final: 0.6673 (ppp) REVERT: A 158 LYS cc_start: 0.6861 (pttt) cc_final: 0.6027 (mttm) REVERT: A 166 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7700 (t80) REVERT: A 295 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8707 (mt) REVERT: E 33 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8725 (m-40) REVERT: E 121 ASN cc_start: 0.6266 (OUTLIER) cc_final: 0.6026 (m-40) REVERT: E 174 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8555 (mmmm) REVERT: E 198 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 476 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8208 (mt-10) REVERT: E 479 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7335 (tppt) REVERT: E 482 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: E 509 MET cc_start: 0.7217 (ptm) cc_final: 0.6793 (ptm) REVERT: E 544 GLU cc_start: 0.8247 (mp0) cc_final: 0.7838 (mt-10) REVERT: E 630 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7776 (ttm110) REVERT: I 121 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.6076 (m-40) REVERT: I 198 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: I 374 ASP cc_start: 0.8197 (t0) cc_final: 0.7813 (t0) REVERT: I 476 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8202 (mt-10) REVERT: I 479 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7451 (tppt) REVERT: I 482 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: I 544 GLU cc_start: 0.8229 (mp0) cc_final: 0.7836 (mt-10) REVERT: M 121 ASN cc_start: 0.6284 (OUTLIER) cc_final: 0.6048 (m-40) REVERT: M 143 ASP cc_start: 0.8369 (t0) cc_final: 0.7776 (m-30) REVERT: M 174 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8484 (mmmm) REVERT: M 198 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: M 374 ASP cc_start: 0.8209 (t0) cc_final: 0.7826 (t0) REVERT: M 476 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8197 (mt-10) REVERT: M 479 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7465 (tppt) REVERT: M 482 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: M 509 MET cc_start: 0.7230 (ptm) cc_final: 0.6752 (ptm) REVERT: F 6 MET cc_start: 0.6918 (ppp) cc_final: 0.6563 (ppp) REVERT: F 158 LYS cc_start: 0.6843 (pttt) cc_final: 0.6013 (mttm) REVERT: F 166 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7635 (t80) REVERT: F 295 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8712 (mt) REVERT: J 6 MET cc_start: 0.6941 (ppp) cc_final: 0.6575 (ppp) REVERT: J 158 LYS cc_start: 0.6866 (pttt) cc_final: 0.6028 (mttm) REVERT: J 166 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7642 (t80) REVERT: J 295 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8711 (mt) REVERT: N 6 MET cc_start: 0.6932 (ppp) cc_final: 0.6573 (ppp) REVERT: N 158 LYS cc_start: 0.6833 (pttt) cc_final: 0.6008 (mttm) REVERT: N 166 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7630 (t80) REVERT: N 295 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8705 (mt) outliers start: 137 outliers final: 80 residues processed: 441 average time/residue: 0.2740 time to fit residues: 199.8534 Evaluate side-chains 432 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 326 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 ASP Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 568 MET Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 419 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 421 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 121 ASN E 65 ASN E 121 ASN I 65 ASN I 121 ASN M 65 ASN M 121 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.146838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101452 restraints weight = 65495.598| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.08 r_work: 0.3156 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45560 Z= 0.138 Angle : 0.522 8.128 63024 Z= 0.284 Chirality : 0.040 0.213 7224 Planarity : 0.003 0.048 6680 Dihedral : 21.271 176.620 9792 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.61 % Favored : 97.20 % Rotamer: Outliers : 3.86 % Allowed : 21.28 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4436 helix: 1.80 (0.11), residues: 2248 sheet: -0.03 (0.21), residues: 604 loop : -0.38 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 630 TYR 0.013 0.001 TYR E 331 PHE 0.019 0.001 PHE E 624 TRP 0.008 0.001 TRP I 559 HIS 0.004 0.001 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00317 (45560) covalent geometry : angle 0.52216 (63024) hydrogen bonds : bond 0.03612 ( 2060) hydrogen bonds : angle 4.01992 ( 5736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 339 time to evaluate : 1.574 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: symmetry clash revert: symmetry clash REVERT: B 33 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (m-40) REVERT: B 121 ASN cc_start: 0.6201 (OUTLIER) cc_final: 0.5770 (m-40) REVERT: B 143 ASP cc_start: 0.8353 (t0) cc_final: 0.7711 (m-30) REVERT: B 174 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8503 (mmmm) REVERT: B 198 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: B 201 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (m) REVERT: B 374 ASP cc_start: 0.8178 (t0) cc_final: 0.7784 (t0) REVERT: B 476 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8205 (mt-10) REVERT: B 479 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7524 (tppt) REVERT: B 482 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: B 509 MET cc_start: 0.7285 (ptm) cc_final: 0.6806 (ptm) REVERT: B 544 GLU cc_start: 0.8270 (mp0) cc_final: 0.7933 (mt-10) REVERT: A 6 MET cc_start: 0.6938 (ppp) cc_final: 0.6682 (ppp) REVERT: A 158 LYS cc_start: 0.6763 (pttt) cc_final: 0.5945 (mttm) REVERT: A 166 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7750 (t80) REVERT: A 295 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8656 (mm) REVERT: E 33 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8757 (m-40) REVERT: E 121 ASN cc_start: 0.6196 (OUTLIER) cc_final: 0.5760 (m-40) REVERT: E 174 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8522 (mmmm) REVERT: E 198 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: E 201 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8061 (m) REVERT: E 374 ASP cc_start: 0.8191 (t0) cc_final: 0.7794 (t0) REVERT: E 476 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8211 (mt-10) REVERT: E 479 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7274 (tppt) REVERT: E 482 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7723 (m-30) REVERT: E 509 MET cc_start: 0.7260 (ptm) cc_final: 0.6824 (ptm) REVERT: E 544 GLU cc_start: 0.8245 (mp0) cc_final: 0.7847 (mt-10) REVERT: I 33 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8759 (m-40) REVERT: I 121 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5793 (m-40) REVERT: I 198 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: I 201 SER cc_start: 0.8335 (OUTLIER) cc_final: 0.8059 (m) REVERT: I 374 ASP cc_start: 0.8168 (t0) cc_final: 0.7804 (t0) REVERT: I 476 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8205 (mt-10) REVERT: I 479 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7535 (tppt) REVERT: I 482 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: I 544 GLU cc_start: 0.8209 (mp0) cc_final: 0.7835 (mt-10) REVERT: M 33 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8786 (m-40) REVERT: M 121 ASN cc_start: 0.6199 (OUTLIER) cc_final: 0.5769 (m-40) REVERT: M 143 ASP cc_start: 0.8336 (t0) cc_final: 0.7688 (m-30) REVERT: M 174 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8493 (mmmm) REVERT: M 198 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: M 201 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.8055 (m) REVERT: M 476 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8204 (mt-10) REVERT: M 479 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7539 (tppt) REVERT: M 482 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: M 509 MET cc_start: 0.7273 (ptm) cc_final: 0.6787 (ptm) REVERT: M 544 GLU cc_start: 0.8300 (mp0) cc_final: 0.7964 (mt-10) REVERT: F 6 MET cc_start: 0.6918 (ppp) cc_final: 0.6666 (ppp) REVERT: F 158 LYS cc_start: 0.6738 (pttt) cc_final: 0.5922 (mttm) REVERT: F 166 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7630 (t80) REVERT: F 295 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8660 (mm) REVERT: J 6 MET cc_start: 0.6931 (ppp) cc_final: 0.6676 (ppp) REVERT: J 158 LYS cc_start: 0.6773 (pttt) cc_final: 0.5949 (mttm) REVERT: J 166 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7648 (t80) REVERT: J 295 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8662 (mm) REVERT: N 6 MET cc_start: 0.6924 (ppp) cc_final: 0.6675 (ppp) REVERT: N 158 LYS cc_start: 0.6741 (pttt) cc_final: 0.5929 (mttm) REVERT: N 166 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7637 (t80) REVERT: N 295 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8700 (mt) outliers start: 160 outliers final: 108 residues processed: 472 average time/residue: 0.2598 time to fit residues: 203.2487 Evaluate side-chains 460 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 321 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 452 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 568 MET Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 371 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 452 ASP Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 568 MET Chi-restraints excluded: chain M residue 642 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 84 optimal weight: 5.9990 chunk 473 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 407 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099006 restraints weight = 65374.283| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.04 r_work: 0.3098 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 45560 Z= 0.228 Angle : 0.581 8.878 63024 Z= 0.312 Chirality : 0.043 0.216 7224 Planarity : 0.004 0.050 6680 Dihedral : 21.293 176.205 9792 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.73 % Favored : 97.02 % Rotamer: Outliers : 4.37 % Allowed : 21.09 % Favored : 74.54 % 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: 0.97 (0.13), residues: 4436 helix: 1.68 (0.11), residues: 2260 sheet: -0.13 (0.21), residues: 604 loop : -0.49 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 630 TYR 0.016 0.002 TYR B 331 PHE 0.017 0.002 PHE E 624 TRP 0.007 0.001 TRP I 559 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00540 (45560) covalent geometry : angle 0.58095 (63024) hydrogen bonds : bond 0.04041 ( 2060) hydrogen bonds : angle 4.11139 ( 5736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 318 time to evaluate : 1.661 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: symmetry clash REVERT: B 33 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8759 (m-40) REVERT: B 121 ASN cc_start: 0.6128 (OUTLIER) cc_final: 0.5703 (m-40) REVERT: B 143 ASP cc_start: 0.8411 (t0) cc_final: 0.7824 (m-30) REVERT: B 174 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8556 (mmmm) REVERT: B 198 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: B 201 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 247 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: B 374 ASP cc_start: 0.8226 (t0) cc_final: 0.7835 (t0) REVERT: B 476 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8226 (mt-10) REVERT: B 479 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7736 (tppt) REVERT: B 482 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: B 509 MET cc_start: 0.7289 (ptm) cc_final: 0.6808 (ptm) REVERT: B 544 GLU cc_start: 0.8300 (mp0) cc_final: 0.7950 (mt-10) REVERT: A 6 MET cc_start: 0.7035 (ppp) cc_final: 0.6799 (ppp) REVERT: A 65 LEU cc_start: 0.8720 (tp) cc_final: 0.8165 (mt) REVERT: A 158 LYS cc_start: 0.6795 (pttt) cc_final: 0.6060 (mttm) REVERT: A 166 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 295 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8746 (mt) REVERT: E 33 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8765 (m-40) REVERT: E 121 ASN cc_start: 0.6158 (OUTLIER) cc_final: 0.5733 (m-40) REVERT: E 174 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8519 (mmmm) REVERT: E 198 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: E 247 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: E 374 ASP cc_start: 0.8219 (t0) cc_final: 0.7830 (t0) REVERT: E 476 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8238 (mt-10) REVERT: E 479 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7572 (tppt) REVERT: E 482 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: E 509 MET cc_start: 0.7269 (ptm) cc_final: 0.6831 (ptm) REVERT: E 544 GLU cc_start: 0.8269 (mp0) cc_final: 0.7866 (mt-10) REVERT: I 33 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8732 (m-40) REVERT: I 121 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5764 (m-40) REVERT: I 198 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: I 201 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (m) REVERT: I 247 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: I 374 ASP cc_start: 0.8233 (t0) cc_final: 0.7862 (t0) REVERT: I 476 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8223 (mt-10) REVERT: I 479 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7743 (tppt) REVERT: I 482 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: I 492 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7365 (mtp180) REVERT: I 544 GLU cc_start: 0.8281 (mp0) cc_final: 0.7944 (mt-10) REVERT: M 33 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8738 (m-40) REVERT: M 121 ASN cc_start: 0.6146 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: M 143 ASP cc_start: 0.8403 (t0) cc_final: 0.7823 (m-30) REVERT: M 174 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8554 (mmmm) REVERT: M 198 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: M 201 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8347 (m) REVERT: M 247 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7736 (mm-30) REVERT: M 476 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8230 (mt-10) REVERT: M 479 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7665 (tppt) REVERT: M 482 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: M 509 MET cc_start: 0.7286 (ptm) cc_final: 0.6802 (ptm) REVERT: M 544 GLU cc_start: 0.8343 (mp0) cc_final: 0.7993 (mt-10) REVERT: F 6 MET cc_start: 0.7018 (ppp) cc_final: 0.6785 (ppp) REVERT: F 65 LEU cc_start: 0.8727 (tp) cc_final: 0.8171 (mt) REVERT: F 158 LYS cc_start: 0.6776 (pttt) cc_final: 0.6042 (mttm) REVERT: F 166 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7625 (t80) REVERT: F 295 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8729 (mt) REVERT: J 6 MET cc_start: 0.7027 (ppp) cc_final: 0.6787 (ppp) REVERT: J 65 LEU cc_start: 0.8723 (tp) cc_final: 0.8162 (mt) REVERT: J 158 LYS cc_start: 0.6800 (pttt) cc_final: 0.6061 (mttm) REVERT: J 166 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7643 (t80) REVERT: J 295 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8730 (mt) REVERT: N 6 MET cc_start: 0.7026 (ppp) cc_final: 0.6794 (ppp) REVERT: N 65 LEU cc_start: 0.8726 (tp) cc_final: 0.8168 (mt) REVERT: N 158 LYS cc_start: 0.6782 (pttt) cc_final: 0.6045 (mttm) REVERT: N 166 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7616 (t80) REVERT: N 295 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8721 (mt) outliers start: 181 outliers final: 128 residues processed: 468 average time/residue: 0.2655 time to fit residues: 204.6938 Evaluate side-chains 476 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 314 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 452 ASP Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 430 ILE Chi-restraints excluded: chain I residue 452 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 568 MET Chi-restraints excluded: chain I residue 642 ILE Chi-restraints excluded: chain I residue 676 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 247 GLU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 371 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 452 ASP Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 568 MET Chi-restraints excluded: chain M residue 642 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 415 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 378 optimal weight: 10.0000 chunk 396 optimal weight: 0.6980 chunk 426 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 318 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 337 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 463 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.146659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101284 restraints weight = 65545.153| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.08 r_work: 0.3154 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 45560 Z= 0.135 Angle : 0.535 9.702 63024 Z= 0.288 Chirality : 0.040 0.212 7224 Planarity : 0.003 0.050 6680 Dihedral : 21.184 176.338 9792 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.71 % Favored : 97.11 % Rotamer: Outliers : 4.05 % Allowed : 21.19 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4436 helix: 1.84 (0.11), residues: 2256 sheet: -0.08 (0.21), residues: 604 loop : -0.46 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 630 TYR 0.013 0.001 TYR M 331 PHE 0.018 0.001 PHE B 624 TRP 0.007 0.001 TRP I 559 HIS 0.004 0.001 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00311 (45560) covalent geometry : angle 0.53467 (63024) hydrogen bonds : bond 0.03586 ( 2060) hydrogen bonds : angle 3.99967 ( 5736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 334 time to evaluate : 1.570 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: symmetry clash revert: symmetry clash REVERT: B 33 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: B 121 ASN cc_start: 0.5962 (OUTLIER) cc_final: 0.5625 (m110) REVERT: B 143 ASP cc_start: 0.8368 (t0) cc_final: 0.7726 (m-30) REVERT: B 174 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8583 (mmmm) REVERT: B 198 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: B 374 ASP cc_start: 0.8193 (t0) cc_final: 0.7819 (t0) REVERT: B 476 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8175 (mt-10) REVERT: B 479 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7517 (tppt) REVERT: B 482 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: B 509 MET cc_start: 0.7294 (ptm) cc_final: 0.6819 (ptm) REVERT: B 544 GLU cc_start: 0.8309 (mp0) cc_final: 0.7931 (mt-10) REVERT: A 6 MET cc_start: 0.7002 (ppp) cc_final: 0.6777 (ppp) REVERT: A 65 LEU cc_start: 0.8702 (tp) cc_final: 0.8153 (mt) REVERT: A 158 LYS cc_start: 0.6684 (pttt) cc_final: 0.5923 (mttm) REVERT: A 166 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7754 (t80) REVERT: A 295 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8667 (mt) REVERT: E 33 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8755 (m-40) REVERT: E 121 ASN cc_start: 0.5969 (OUTLIER) cc_final: 0.5661 (m110) REVERT: E 174 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8485 (mmmm) REVERT: E 198 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 247 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: E 374 ASP cc_start: 0.8181 (t0) cc_final: 0.7803 (t0) REVERT: E 476 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8228 (mt-10) REVERT: E 479 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7530 (tppt) REVERT: E 482 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: E 509 MET cc_start: 0.7280 (ptm) cc_final: 0.6840 (ptm) REVERT: E 544 GLU cc_start: 0.8282 (mp0) cc_final: 0.7851 (mt-10) REVERT: I 33 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8743 (m-40) REVERT: I 121 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.5769 (m-40) REVERT: I 198 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: I 247 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: I 374 ASP cc_start: 0.8175 (t0) cc_final: 0.7813 (t0) REVERT: I 476 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8172 (mt-10) REVERT: I 479 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7540 (tppt) REVERT: I 482 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: I 497 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8447 (mm) REVERT: I 544 GLU cc_start: 0.8231 (mp0) cc_final: 0.7838 (mt-10) REVERT: M 33 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8795 (m-40) REVERT: M 121 ASN cc_start: 0.5951 (OUTLIER) cc_final: 0.5649 (m110) REVERT: M 143 ASP cc_start: 0.8368 (t0) cc_final: 0.7728 (m-30) REVERT: M 174 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8523 (mmmm) REVERT: M 198 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: M 247 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: M 374 ASP cc_start: 0.8181 (t0) cc_final: 0.7798 (t0) REVERT: M 476 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8176 (mt-10) REVERT: M 479 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7615 (tppt) REVERT: M 482 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: M 509 MET cc_start: 0.7290 (ptm) cc_final: 0.6810 (ptm) REVERT: M 544 GLU cc_start: 0.8309 (mp0) cc_final: 0.7970 (mt-10) REVERT: F 6 MET cc_start: 0.6910 (ppp) cc_final: 0.6709 (ppp) REVERT: F 65 LEU cc_start: 0.8715 (tp) cc_final: 0.8162 (mt) REVERT: F 158 LYS cc_start: 0.6660 (pttt) cc_final: 0.5903 (mttm) REVERT: F 166 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7700 (t80) REVERT: F 295 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8699 (mm) REVERT: J 6 MET cc_start: 0.6994 (ppp) cc_final: 0.6764 (ppp) REVERT: J 65 LEU cc_start: 0.8701 (tp) cc_final: 0.8146 (mt) REVERT: J 158 LYS cc_start: 0.6680 (pttt) cc_final: 0.5915 (mttm) REVERT: J 166 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7703 (t80) REVERT: J 295 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8696 (mm) REVERT: N 6 MET cc_start: 0.6988 (ppp) cc_final: 0.6761 (ppp) REVERT: N 65 LEU cc_start: 0.8705 (tp) cc_final: 0.8155 (mt) REVERT: N 158 LYS cc_start: 0.6671 (pttt) cc_final: 0.5904 (mttm) REVERT: N 166 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.7691 (t80) REVERT: N 295 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8684 (mm) outliers start: 168 outliers final: 119 residues processed: 478 average time/residue: 0.2605 time to fit residues: 204.8244 Evaluate side-chains 471 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 321 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 198 GLU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 452 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 497 LEU Chi-restraints excluded: chain I residue 568 MET Chi-restraints excluded: chain I residue 642 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 198 GLU Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 247 GLU Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 568 MET Chi-restraints excluded: chain M residue 642 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 386 optimal weight: 0.9990 chunk 403 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 335 optimal weight: 0.0970 chunk 370 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 407 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102011 restraints weight = 65034.833| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.07 r_work: 0.3169 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45560 Z= 0.125 Angle : 0.530 9.483 63024 Z= 0.285 Chirality : 0.040 0.295 7224 Planarity : 0.003 0.050 6680 Dihedral : 21.103 176.718 9792 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 3.76 % Allowed : 21.31 % Favored : 74.93 % 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: 1.23 (0.13), residues: 4436 helix: 1.92 (0.11), residues: 2256 sheet: 0.04 (0.21), residues: 604 loop : -0.44 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 492 TYR 0.019 0.001 TYR I 457 PHE 0.018 0.001 PHE M 624 TRP 0.008 0.001 TRP M 559 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00283 (45560) covalent geometry : angle 0.52983 (63024) hydrogen bonds : bond 0.03447 ( 2060) hydrogen bonds : angle 3.94604 ( 5736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 340 time to evaluate : 1.195 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: symmetry clash REVERT: B 121 ASN cc_start: 0.5988 (OUTLIER) cc_final: 0.5685 (m-40) REVERT: B 143 ASP cc_start: 0.8292 (t0) cc_final: 0.7651 (m-30) REVERT: B 174 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8561 (mmmm) REVERT: B 247 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: B 374 ASP cc_start: 0.8187 (t0) cc_final: 0.7814 (t0) REVERT: B 476 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8179 (mt-10) REVERT: B 479 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7506 (tppt) REVERT: B 482 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: B 509 MET cc_start: 0.7278 (ptm) cc_final: 0.6802 (ptm) REVERT: B 544 GLU cc_start: 0.8333 (mp0) cc_final: 0.7931 (mt-10) REVERT: B 582 MET cc_start: 0.5886 (mmt) cc_final: 0.5406 (mmm) REVERT: A 6 MET cc_start: 0.6998 (ppp) cc_final: 0.6795 (ppp) REVERT: A 65 LEU cc_start: 0.8699 (tp) cc_final: 0.8154 (mt) REVERT: A 158 LYS cc_start: 0.6722 (pttt) cc_final: 0.6069 (mttm) REVERT: A 166 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 295 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8657 (mm) REVERT: E 121 ASN cc_start: 0.6016 (OUTLIER) cc_final: 0.5738 (m110) REVERT: E 174 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8486 (mmmm) REVERT: E 198 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 247 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: E 374 ASP cc_start: 0.8172 (t0) cc_final: 0.7796 (t0) REVERT: E 476 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8204 (mt-10) REVERT: E 479 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7527 (tppt) REVERT: E 482 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: E 509 MET cc_start: 0.7262 (ptm) cc_final: 0.6821 (ptm) REVERT: E 544 GLU cc_start: 0.8291 (mp0) cc_final: 0.7858 (mt-10) REVERT: I 121 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5735 (m110) REVERT: I 247 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: I 374 ASP cc_start: 0.8179 (t0) cc_final: 0.7825 (t0) REVERT: I 476 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8182 (mt-10) REVERT: I 479 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7604 (tppt) REVERT: I 482 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: I 544 GLU cc_start: 0.8279 (mp0) cc_final: 0.7866 (mt-10) REVERT: I 582 MET cc_start: 0.5877 (mmt) cc_final: 0.5399 (mmm) REVERT: M 121 ASN cc_start: 0.5985 (OUTLIER) cc_final: 0.5714 (m110) REVERT: M 143 ASP cc_start: 0.8298 (t0) cc_final: 0.7654 (m-30) REVERT: M 174 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8500 (mmmm) REVERT: M 374 ASP cc_start: 0.8181 (t0) cc_final: 0.7804 (t0) REVERT: M 476 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8182 (mt-10) REVERT: M 479 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7529 (tppt) REVERT: M 482 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: M 509 MET cc_start: 0.7281 (ptm) cc_final: 0.6800 (ptm) REVERT: M 544 GLU cc_start: 0.8366 (mp0) cc_final: 0.7964 (mt-10) REVERT: M 582 MET cc_start: 0.5807 (mmt) cc_final: 0.5326 (mmm) REVERT: F 6 MET cc_start: 0.6981 (ppp) cc_final: 0.6774 (ppp) REVERT: F 65 LEU cc_start: 0.8710 (tp) cc_final: 0.8160 (mt) REVERT: F 158 LYS cc_start: 0.6692 (pttt) cc_final: 0.6065 (mttm) REVERT: F 166 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7710 (t80) REVERT: F 295 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8673 (mm) REVERT: J 6 MET cc_start: 0.6988 (ppp) cc_final: 0.6783 (ppp) REVERT: J 65 LEU cc_start: 0.8703 (tp) cc_final: 0.8149 (mt) REVERT: J 158 LYS cc_start: 0.6727 (pttt) cc_final: 0.6077 (mttm) REVERT: J 166 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7717 (t80) REVERT: J 295 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8661 (mm) REVERT: N 6 MET cc_start: 0.6989 (ppp) cc_final: 0.6782 (ppp) REVERT: N 65 LEU cc_start: 0.8703 (tp) cc_final: 0.8153 (mt) REVERT: N 158 LYS cc_start: 0.6705 (pttt) cc_final: 0.6061 (mttm) REVERT: N 166 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7704 (t80) REVERT: N 295 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8656 (mm) outliers start: 156 outliers final: 118 residues processed: 472 average time/residue: 0.2351 time to fit residues: 182.3126 Evaluate side-chains 463 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 322 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 568 MET Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 452 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 568 MET Chi-restraints excluded: chain I residue 642 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 371 THR Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 568 MET Chi-restraints excluded: chain M residue 642 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 358 optimal weight: 4.9990 chunk 360 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 350 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100077 restraints weight = 65519.979| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.06 r_work: 0.3110 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 45560 Z= 0.198 Angle : 0.571 9.652 63024 Z= 0.306 Chirality : 0.042 0.252 7224 Planarity : 0.004 0.051 6680 Dihedral : 21.127 176.358 9792 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.73 % Favored : 97.02 % Rotamer: Outliers : 3.60 % Allowed : 21.60 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.13), residues: 4436 helix: 1.78 (0.11), residues: 2260 sheet: -0.05 (0.21), residues: 604 loop : -0.49 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 630 TYR 0.021 0.002 TYR B 457 PHE 0.017 0.001 PHE E 624 TRP 0.006 0.001 TRP B 559 HIS 0.003 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00467 (45560) covalent geometry : angle 0.57069 (63024) hydrogen bonds : bond 0.03820 ( 2060) hydrogen bonds : angle 4.03833 ( 5736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 324 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5837 (m-40) REVERT: B 143 ASP cc_start: 0.8370 (t0) cc_final: 0.7780 (m-30) REVERT: B 174 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8583 (mmmm) REVERT: B 247 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: B 374 ASP cc_start: 0.8235 (t0) cc_final: 0.7866 (t0) REVERT: B 479 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7592 (tppt) REVERT: B 482 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: B 509 MET cc_start: 0.7273 (ptm) cc_final: 0.6805 (ptm) REVERT: B 544 GLU cc_start: 0.8345 (mp0) cc_final: 0.7953 (mt-10) REVERT: B 582 MET cc_start: 0.5919 (mmt) cc_final: 0.5477 (mmm) REVERT: A 65 LEU cc_start: 0.8706 (tp) cc_final: 0.8177 (mt) REVERT: A 158 LYS cc_start: 0.6794 (pttt) cc_final: 0.6071 (mttm) REVERT: A 166 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7672 (t80) REVERT: A 295 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8661 (mm) REVERT: E 33 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8697 (m-40) REVERT: E 121 ASN cc_start: 0.6161 (OUTLIER) cc_final: 0.5816 (m-40) REVERT: E 174 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8477 (mmmm) REVERT: E 198 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: E 247 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: E 374 ASP cc_start: 0.8223 (t0) cc_final: 0.7837 (t0) REVERT: E 479 LYS cc_start: 0.8174 (mtpt) cc_final: 0.7559 (tppt) REVERT: E 482 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: E 509 MET cc_start: 0.7276 (ptm) cc_final: 0.6826 (ptm) REVERT: E 544 GLU cc_start: 0.8318 (mp0) cc_final: 0.7876 (mt-10) REVERT: I 121 ASN cc_start: 0.6169 (OUTLIER) cc_final: 0.5830 (m-40) REVERT: I 247 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: I 374 ASP cc_start: 0.8230 (t0) cc_final: 0.7874 (t0) REVERT: I 476 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8201 (mt-10) REVERT: I 479 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7607 (tppt) REVERT: I 482 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: I 544 GLU cc_start: 0.8385 (mp0) cc_final: 0.7949 (mt-10) REVERT: I 582 MET cc_start: 0.5891 (mmt) cc_final: 0.5419 (mmm) REVERT: M 121 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5839 (m-40) REVERT: M 143 ASP cc_start: 0.8374 (t0) cc_final: 0.7788 (m-30) REVERT: M 174 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8526 (mmmm) REVERT: M 247 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: M 374 ASP cc_start: 0.8234 (t0) cc_final: 0.7859 (t0) REVERT: M 479 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7620 (tppt) REVERT: M 482 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: M 509 MET cc_start: 0.7283 (ptm) cc_final: 0.6810 (ptm) REVERT: M 544 GLU cc_start: 0.8390 (mp0) cc_final: 0.7957 (mt-10) REVERT: M 582 MET cc_start: 0.5855 (mmt) cc_final: 0.5395 (mmm) REVERT: F 65 LEU cc_start: 0.8709 (tp) cc_final: 0.8174 (mt) REVERT: F 158 LYS cc_start: 0.6772 (pttt) cc_final: 0.6053 (mttm) REVERT: F 166 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7624 (t80) REVERT: F 295 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8671 (mm) REVERT: J 65 LEU cc_start: 0.8708 (tp) cc_final: 0.8172 (mt) REVERT: J 158 LYS cc_start: 0.6791 (pttt) cc_final: 0.6068 (mttm) REVERT: J 166 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7632 (t80) REVERT: J 295 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8669 (mm) REVERT: N 65 LEU cc_start: 0.8706 (tp) cc_final: 0.8173 (mt) REVERT: N 158 LYS cc_start: 0.6786 (pttt) cc_final: 0.6065 (mttm) REVERT: N 166 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7615 (t80) REVERT: N 295 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8666 (mm) outliers start: 149 outliers final: 121 residues processed: 457 average time/residue: 0.2065 time to fit residues: 155.7758 Evaluate side-chains 454 residues out of total 4144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 308 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 182 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 540 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 158 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 174 LYS Chi-restraints excluded: chain E residue 182 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 380 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 482 ASP Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 602 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 121 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 182 PHE Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 275 THR Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 305 LYS Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 380 ILE Chi-restraints excluded: chain I residue 431 LEU Chi-restraints excluded: chain I residue 452 ASP Chi-restraints excluded: chain I residue 482 ASP Chi-restraints excluded: chain I residue 568 MET Chi-restraints excluded: chain I residue 642 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 182 PHE Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 235 VAL Chi-restraints excluded: chain M residue 243 VAL Chi-restraints excluded: chain M residue 247 GLU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain M residue 275 THR Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 305 LYS Chi-restraints excluded: chain M residue 380 ILE Chi-restraints excluded: chain M residue 431 LEU Chi-restraints excluded: chain M residue 452 ASP Chi-restraints excluded: chain M residue 482 ASP Chi-restraints excluded: chain M residue 540 THR Chi-restraints excluded: chain M residue 642 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 166 PHE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 295 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 166 PHE Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 354 ILE Chi-restraints excluded: chain N residue 17 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 92 LYS Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 161 ILE Chi-restraints excluded: chain N residue 166 PHE Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 233 ILE Chi-restraints excluded: chain N residue 295 ILE Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 269 optimal weight: 1.9990 chunk 401 optimal weight: 0.3980 chunk 353 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 458 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 381 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN E 121 ASN I 121 ASN M 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102258 restraints weight = 65459.009| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.08 r_work: 0.3157 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 45560 Z= 0.126 Angle : 0.542 9.118 63024 Z= 0.291 Chirality : 0.040 0.251 7224 Planarity : 0.003 0.050 6680 Dihedral : 21.049 176.489 9792 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.77 % Favored : 97.05 % Rotamer: Outliers : 3.45 % Allowed : 21.84 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4436 helix: 1.89 (0.11), residues: 2260 sheet: 0.24 (0.22), residues: 564 loop : -0.45 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 630 TYR 0.025 0.001 TYR B 457 PHE 0.018 0.001 PHE M 624 TRP 0.010 0.001 TRP B 559 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00287 (45560) covalent geometry : angle 0.54170 (63024) hydrogen bonds : bond 0.03440 ( 2060) hydrogen bonds : angle 3.95741 ( 5736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11580.04 seconds wall clock time: 198 minutes 59.97 seconds (11939.97 seconds total)