Starting phenix.real_space_refine on Sun Aug 9 20:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.map" model { file = "/net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lbq_62954/08_2026/9lbq_62954.cif" } resolution = 2.94 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= 0.001 sd= 0.024 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 324 5.49 5 S 80 5.16 5 C 23016 2.51 5 N 6392 2.21 5 O 7840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37652 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2577 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 10, 'TRANS': 308} Chain breaks: 3 Chain: "B" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5123 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 18, 'TRANS': 602} Chain breaks: 4 Chain: "C" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1346 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 24} Link IDs: {'rna2p': 6, 'rna3p': 56} Chain breaks: 1 Chain: "D" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain breaks: 1 Restraints were copied for chains: E, I, M, F, J, N, G, K, O, H, L, P Time building chain proxies: 8.32, per 1000 atoms: 0.22 Number of scatterers: 37652 At special positions: 0 Unit cell: (103.375, 186.902, 236.522, 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 80 16.00 P 324 15.00 O 7840 8.00 N 6392 7.00 C 23016 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: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7240 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 32 sheets defined 56.6% alpha, 11.9% beta 84 base pairs and 180 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.774A pdb=" N HIS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 removed outlier: 4.025A pdb=" N ILE A 75 " --> pdb=" O LEU A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'A' and resid 139 through 146 Processing helix chain 'A' and resid 168 through 192 removed outlier: 4.936A pdb=" N LYS A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N MET A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.985A pdb=" N ILE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 283 removed outlier: 3.695A pdb=" N LEU A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.593A pdb=" N ILE A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 344 removed outlier: 3.610A pdb=" N LEU A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 371 removed outlier: 3.592A pdb=" N ASN A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 removed outlier: 3.526A pdb=" N LYS B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 90 through 107 removed outlier: 5.624A pdb=" N SER B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 removed outlier: 4.034A 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 259 through 276 removed outlier: 4.169A pdb=" N THR B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.669A pdb=" N VAL B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.713A pdb=" N LEU B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 removed outlier: 3.555A pdb=" N LEU B 378 " --> pdb=" O ASP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 388 removed outlier: 3.712A pdb=" N LEU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 removed outlier: 3.844A pdb=" N LEU B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 417 through 421 removed outlier: 3.523A pdb=" N LEU B 420 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.724A pdb=" N LYS B 440 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 485 through 500 removed outlier: 4.119A pdb=" N GLY B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 removed outlier: 3.624A pdb=" N LEU B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 530 " --> pdb=" O ARG B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 548 Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.318A pdb=" N MET B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 586 removed outlier: 4.009A pdb=" N PHE B 578 " --> pdb=" O ASN B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 removed outlier: 3.719A pdb=" N LEU B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.888A pdb=" N PHE B 636 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 650 removed outlier: 3.585A pdb=" N PHE B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 667 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 687 through 691 Processing helix chain 'B' and resid 696 through 713 removed outlier: 3.576A 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 744 removed outlier: 3.691A pdb=" N GLU B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.775A pdb=" N HIS E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 63 " --> pdb=" O PRO E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 75 removed outlier: 4.025A pdb=" N ILE E 75 " --> pdb=" O LEU E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 116 through 124 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 168 through 192 removed outlier: 4.936A pdb=" N LYS E 179 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N MET E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 227 removed outlier: 3.985A pdb=" N ILE E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 283 removed outlier: 3.695A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.594A pdb=" N ILE E 290 " --> pdb=" O PRO E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 344 removed outlier: 3.609A pdb=" N LEU E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 371 removed outlier: 3.592A pdb=" N ASN E 371 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 51 removed outlier: 3.527A pdb=" N LYS F 36 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 51 " --> pdb=" O TYR F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 90 through 107 removed outlier: 5.624A pdb=" N SER F 103 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS F 107 " --> pdb=" O SER F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 4.035A pdb=" N ARG F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 259 through 276 removed outlier: 4.170A pdb=" N THR F 275 " --> pdb=" O THR F 271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 310 removed outlier: 3.669A pdb=" N VAL F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 346 removed outlier: 3.712A pdb=" N LEU F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 380 removed outlier: 3.554A pdb=" N LEU F 378 " --> pdb=" O ASP F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 388 removed outlier: 3.711A pdb=" N LEU F 388 " --> pdb=" O ASN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 407 removed outlier: 3.844A pdb=" N LEU F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 413 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.522A pdb=" N LEU F 420 " --> pdb=" O ALA F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 434 Processing helix chain 'F' and resid 435 through 440 removed outlier: 3.725A pdb=" N LYS F 440 " --> pdb=" O GLY F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'F' and resid 485 through 500 removed outlier: 4.120A pdb=" N GLY F 489 " --> pdb=" O ASP F 485 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 491 " --> pdb=" O GLY F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 532 removed outlier: 3.625A pdb=" N LEU F 523 " --> pdb=" O SER F 519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 548 Processing helix chain 'F' and resid 552 through 568 removed outlier: 4.319A pdb=" N MET F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 586 removed outlier: 4.008A pdb=" N PHE F 578 " --> pdb=" O ASN F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 600 removed outlier: 3.718A pdb=" N LEU F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 636 removed outlier: 3.887A pdb=" N PHE F 636 " --> pdb=" O VAL F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 650 removed outlier: 3.586A pdb=" N PHE F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 659 through 667 Processing helix chain 'F' and resid 669 through 683 Processing helix chain 'F' and resid 687 through 691 Processing helix chain 'F' and resid 696 through 713 removed outlier: 3.577A pdb=" N THR F 700 " --> pdb=" O GLY F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 727 Processing helix chain 'F' and resid 727 through 744 removed outlier: 3.690A pdb=" N GLU F 744 " --> pdb=" O SER F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 749 Processing helix chain 'I' and resid 58 through 71 removed outlier: 3.774A pdb=" N HIS I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL I 63 " --> pdb=" O PRO I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 75 removed outlier: 4.026A pdb=" N ILE I 75 " --> pdb=" O LEU I 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 72 through 75' Processing helix chain 'I' and resid 89 through 95 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 168 through 192 removed outlier: 4.936A pdb=" N LYS I 179 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N MET I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 227 removed outlier: 3.986A pdb=" N ILE I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 283 removed outlier: 3.696A pdb=" N LEU I 275 " --> pdb=" O LEU I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 295 removed outlier: 3.594A pdb=" N ILE I 290 " --> pdb=" O PRO I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 344 removed outlier: 3.610A pdb=" N LEU I 336 " --> pdb=" O TYR I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 371 removed outlier: 3.593A pdb=" N ASN I 371 " --> pdb=" O LYS I 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 51 removed outlier: 3.527A pdb=" N LYS J 36 " --> pdb=" O ASN J 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU J 51 " --> pdb=" O TYR J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 84 Processing helix chain 'J' and resid 90 through 107 removed outlier: 5.624A pdb=" N SER J 103 " --> pdb=" O THR J 99 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N SER J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS J 107 " --> pdb=" O SER J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 154 removed outlier: 4.034A pdb=" N ARG J 147 " --> pdb=" O ASP J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'J' and resid 259 through 276 removed outlier: 4.169A pdb=" N THR J 275 " --> pdb=" O THR J 271 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU J 276 " --> pdb=" O LEU J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 310 removed outlier: 3.670A pdb=" N VAL J 300 " --> pdb=" O ALA J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 346 removed outlier: 3.712A pdb=" N LEU J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 380 removed outlier: 3.554A pdb=" N LEU J 378 " --> pdb=" O ASP J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 388 removed outlier: 3.712A pdb=" N LEU J 388 " --> pdb=" O ASN J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 407 removed outlier: 3.844A pdb=" N LEU J 403 " --> pdb=" O GLY J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 413 Processing helix chain 'J' and resid 417 through 421 removed outlier: 3.523A pdb=" N LEU J 420 " --> pdb=" O ALA J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 434 Processing helix chain 'J' and resid 435 through 440 removed outlier: 3.725A pdb=" N LYS J 440 " --> pdb=" O GLY J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 477 Processing helix chain 'J' and resid 485 through 500 removed outlier: 4.118A pdb=" N GLY J 489 " --> pdb=" O ASP J 485 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG J 490 " --> pdb=" O THR J 486 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL J 491 " --> pdb=" O GLY J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 532 removed outlier: 3.625A pdb=" N LEU J 523 " --> pdb=" O SER J 519 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL J 530 " --> pdb=" O ARG J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 542 through 548 Processing helix chain 'J' and resid 552 through 568 removed outlier: 4.319A pdb=" N MET J 568 " --> pdb=" O ILE J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 586 removed outlier: 4.008A pdb=" N PHE J 578 " --> pdb=" O ASN J 574 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 600 removed outlier: 3.717A pdb=" N LEU J 595 " --> pdb=" O GLN J 591 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 636 removed outlier: 3.887A pdb=" N PHE J 636 " --> pdb=" O VAL J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 639 through 650 removed outlier: 3.585A pdb=" N PHE J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 659 through 667 Processing helix chain 'J' and resid 669 through 683 Processing helix chain 'J' and resid 687 through 691 Processing helix chain 'J' and resid 696 through 713 removed outlier: 3.577A pdb=" N THR J 700 " --> pdb=" O GLY J 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 715 through 727 Processing helix chain 'J' and resid 727 through 744 removed outlier: 3.690A pdb=" N GLU J 744 " --> pdb=" O SER J 740 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 749 Processing helix chain 'M' and resid 58 through 71 removed outlier: 3.773A pdb=" N HIS M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 75 removed outlier: 4.026A pdb=" N ILE M 75 " --> pdb=" O LEU M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 72 through 75' Processing helix chain 'M' and resid 89 through 95 Processing helix chain 'M' and resid 96 through 98 No H-bonds generated for 'chain 'M' and resid 96 through 98' Processing helix chain 'M' and resid 116 through 124 Processing helix chain 'M' and resid 139 through 146 Processing helix chain 'M' and resid 168 through 192 removed outlier: 4.936A pdb=" N LYS M 179 " --> pdb=" O ILE M 175 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N MET M 180 " --> pdb=" O VAL M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 227 removed outlier: 3.984A pdb=" N ILE M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 283 removed outlier: 3.695A pdb=" N LEU M 275 " --> pdb=" O LEU M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 295 removed outlier: 3.593A pdb=" N ILE M 290 " --> pdb=" O PRO M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 344 removed outlier: 3.610A pdb=" N LEU M 336 " --> pdb=" O TYR M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 371 removed outlier: 3.592A pdb=" N ASN M 371 " --> pdb=" O LYS M 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 51 removed outlier: 3.526A pdb=" N LYS N 36 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 84 Processing helix chain 'N' and resid 90 through 107 removed outlier: 5.624A pdb=" N SER N 103 " --> pdb=" O THR N 99 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER N 104 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 154 removed outlier: 4.034A pdb=" N ARG N 147 " --> pdb=" O ASP N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 164 No H-bonds generated for 'chain 'N' and resid 162 through 164' Processing helix chain 'N' and resid 259 through 276 removed outlier: 4.170A pdb=" N THR N 275 " --> pdb=" O THR N 271 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU N 276 " --> pdb=" O LEU N 272 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 310 removed outlier: 3.667A pdb=" N VAL N 300 " --> pdb=" O ALA N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 346 removed outlier: 3.713A pdb=" N LEU N 339 " --> pdb=" O SER N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 380 removed outlier: 3.555A pdb=" N LEU N 378 " --> pdb=" O ASP N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 382 through 388 removed outlier: 3.710A pdb=" N LEU N 388 " --> pdb=" O ASN N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 399 through 407 removed outlier: 3.844A pdb=" N LEU N 403 " --> pdb=" O GLY N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 413 Processing helix chain 'N' and resid 417 through 421 removed outlier: 3.522A pdb=" N LEU N 420 " --> pdb=" O ALA N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 434 Processing helix chain 'N' and resid 435 through 440 removed outlier: 3.725A pdb=" N LYS N 440 " --> pdb=" O GLY N 437 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 477 Processing helix chain 'N' and resid 485 through 500 removed outlier: 4.119A pdb=" N GLY N 489 " --> pdb=" O ASP N 485 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG N 490 " --> pdb=" O THR N 486 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL N 491 " --> pdb=" O GLY N 487 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 532 removed outlier: 3.624A pdb=" N LEU N 523 " --> pdb=" O SER N 519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL N 530 " --> pdb=" O ARG N 526 " (cutoff:3.500A) Processing helix chain 'N' and resid 542 through 548 Processing helix chain 'N' and resid 552 through 568 removed outlier: 4.318A pdb=" N MET N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 574 through 586 removed outlier: 4.008A pdb=" N PHE N 578 " --> pdb=" O ASN N 574 " (cutoff:3.500A) Processing helix chain 'N' and resid 591 through 600 removed outlier: 3.719A pdb=" N LEU N 595 " --> pdb=" O GLN N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 636 removed outlier: 3.888A pdb=" N PHE N 636 " --> pdb=" O VAL N 632 " (cutoff:3.500A) Processing helix chain 'N' and resid 639 through 650 removed outlier: 3.586A pdb=" N PHE N 650 " --> pdb=" O LEU N 646 " (cutoff:3.500A) Processing helix chain 'N' and resid 659 through 667 Processing helix chain 'N' and resid 669 through 683 Processing helix chain 'N' and resid 687 through 691 Processing helix chain 'N' and resid 696 through 713 removed outlier: 3.576A pdb=" N THR N 700 " --> pdb=" O GLY N 696 " (cutoff:3.500A) Processing helix chain 'N' and resid 715 through 727 Processing helix chain 'N' and resid 727 through 744 removed outlier: 3.690A pdb=" N GLU N 744 " --> pdb=" O SER N 740 " (cutoff:3.500A) Processing helix chain 'N' and resid 744 through 749 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 198 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA4, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 20 removed outlier: 7.092A pdb=" N ASP B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR B 73 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 6 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL B 8 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU B 69 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.279A pdb=" N VAL B 282 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER B 332 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 284 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 25 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B 353 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS B 27 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE B 355 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE B 29 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N LYS B 357 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 352 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 422 through 425 removed outlier: 6.528A pdb=" N ILE B 394 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE B 448 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE B 396 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP B 450 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR B 537 " --> pdb=" O PHE B 445 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 447 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET B 539 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS B 449 " --> pdb=" O MET B 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 457 Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 46 Processing sheet with id=AB1, first strand: chain 'E' and resid 194 through 198 Processing sheet with id=AB2, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AB3, first strand: chain 'E' and resid 244 through 247 Processing sheet with id=AB4, first strand: chain 'F' and resid 14 through 20 removed outlier: 7.093A pdb=" N ASP F 15 " --> pdb=" O ASN F 10 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR F 73 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE F 6 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR F 71 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL F 8 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLU F 69 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 156 through 160 removed outlier: 6.281A pdb=" N VAL F 282 " --> pdb=" O PHE F 330 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER F 332 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE F 284 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 25 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU F 353 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS F 27 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE F 355 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE F 29 " --> pdb=" O PHE F 355 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N LYS F 357 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL F 352 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 422 through 425 removed outlier: 6.528A pdb=" N ILE F 394 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE F 448 " --> pdb=" O ILE F 394 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE F 396 " --> pdb=" O ILE F 448 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ASP F 450 " --> pdb=" O PHE F 396 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR F 537 " --> pdb=" O PHE F 445 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 447 " --> pdb=" O TYR F 537 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET F 539 " --> pdb=" O ILE F 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS F 449 " --> pdb=" O MET F 539 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 455 through 457 Processing sheet with id=AB8, first strand: chain 'I' and resid 41 through 46 Processing sheet with id=AB9, first strand: chain 'I' and resid 194 through 198 Processing sheet with id=AC1, first strand: chain 'I' and resid 150 through 151 Processing sheet with id=AC2, first strand: chain 'I' and resid 244 through 247 Processing sheet with id=AC3, first strand: chain 'J' and resid 14 through 20 removed outlier: 7.092A pdb=" N ASP J 15 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR J 73 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE J 6 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR J 71 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL J 8 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU J 69 " --> pdb=" O VAL J 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 156 through 160 removed outlier: 6.280A pdb=" N VAL J 282 " --> pdb=" O PHE J 330 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N SER J 332 " --> pdb=" O VAL J 282 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE J 284 " --> pdb=" O SER J 332 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE J 25 " --> pdb=" O GLN J 351 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU J 353 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS J 27 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE J 355 " --> pdb=" O CYS J 27 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ILE J 29 " --> pdb=" O PHE J 355 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N LYS J 357 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL J 352 " --> pdb=" O ILE J 368 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 422 through 425 removed outlier: 6.528A pdb=" N ILE J 394 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE J 448 " --> pdb=" O ILE J 394 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE J 396 " --> pdb=" O ILE J 448 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASP J 450 " --> pdb=" O PHE J 396 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR J 537 " --> pdb=" O PHE J 445 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE J 447 " --> pdb=" O TYR J 537 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET J 539 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS J 449 " --> pdb=" O MET J 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 455 through 457 Processing sheet with id=AC7, first strand: chain 'M' and resid 41 through 46 Processing sheet with id=AC8, first strand: chain 'M' and resid 194 through 198 Processing sheet with id=AC9, first strand: chain 'M' and resid 150 through 151 Processing sheet with id=AD1, first strand: chain 'M' and resid 244 through 247 Processing sheet with id=AD2, first strand: chain 'N' and resid 14 through 20 removed outlier: 7.093A pdb=" N ASP N 15 " --> pdb=" O ASN N 10 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR N 73 " --> pdb=" O GLU N 4 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE N 6 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL N 8 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU N 69 " --> pdb=" O VAL N 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 156 through 160 removed outlier: 6.279A pdb=" N VAL N 282 " --> pdb=" O PHE N 330 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER N 332 " --> pdb=" O VAL N 282 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE N 284 " --> pdb=" O SER N 332 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE N 25 " --> pdb=" O GLN N 351 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU N 353 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS N 27 " --> pdb=" O LEU N 353 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE N 355 " --> pdb=" O CYS N 27 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE N 29 " --> pdb=" O PHE N 355 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYS N 357 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL N 352 " --> pdb=" O ILE N 368 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 422 through 425 removed outlier: 6.528A pdb=" N ILE N 394 " --> pdb=" O VAL N 446 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE N 448 " --> pdb=" O ILE N 394 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE N 396 " --> pdb=" O ILE N 448 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASP N 450 " --> pdb=" O PHE N 396 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR N 537 " --> pdb=" O PHE N 445 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE N 447 " --> pdb=" O TYR N 537 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N MET N 539 " --> pdb=" O ILE N 447 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYS N 449 " --> pdb=" O MET N 539 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 455 through 457 1568 hydrogen bonds defined for protein. 4536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 204 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 180 stacking parallelities Total time for adding SS restraints: 9.58 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6355 1.33 - 1.45: 11745 1.45 - 1.57: 20250 1.57 - 1.69: 582 1.69 - 1.81: 136 Bond restraints: 39068 Sorted by residual: bond pdb=" C1' A C 17 " pdb=" N9 A C 17 " ideal model delta sigma weight residual 1.483 1.378 0.105 1.50e-02 4.44e+03 4.92e+01 bond pdb=" C1' A K 17 " pdb=" N9 A K 17 " ideal model delta sigma weight residual 1.483 1.378 0.105 1.50e-02 4.44e+03 4.90e+01 bond pdb=" C1' A O 17 " pdb=" N9 A O 17 " ideal model delta sigma weight residual 1.483 1.378 0.105 1.50e-02 4.44e+03 4.89e+01 bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.483 1.378 0.105 1.50e-02 4.44e+03 4.88e+01 bond pdb=" O3' A K 19 " pdb=" P A K 20 " ideal model delta sigma weight residual 1.607 1.543 0.064 1.20e-02 6.94e+03 2.83e+01 ... (remaining 39063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 52645 2.26 - 4.52: 1243 4.52 - 6.77: 172 6.77 - 9.03: 56 9.03 - 11.29: 16 Bond angle restraints: 54132 Sorted by residual: angle pdb=" O3' C K 66 " pdb=" C3' C K 66 " pdb=" C2' C K 66 " ideal model delta sigma weight residual 113.70 104.32 9.38 1.60e+00 3.91e-01 3.44e+01 angle pdb=" O3' C O 66 " pdb=" C3' C O 66 " pdb=" C2' C O 66 " ideal model delta sigma weight residual 113.70 104.35 9.35 1.60e+00 3.91e-01 3.41e+01 angle pdb=" O3' C C 66 " pdb=" C3' C C 66 " pdb=" C2' C C 66 " ideal model delta sigma weight residual 113.70 104.37 9.33 1.60e+00 3.91e-01 3.40e+01 angle pdb=" O3' C G 66 " pdb=" C3' C G 66 " pdb=" C2' C G 66 " ideal model delta sigma weight residual 113.70 104.40 9.30 1.60e+00 3.91e-01 3.38e+01 angle pdb=" O3' C O 67 " pdb=" C3' C O 67 " pdb=" C2' C O 67 " ideal model delta sigma weight residual 113.70 105.25 8.45 1.60e+00 3.91e-01 2.79e+01 ... (remaining 54127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 21663 31.31 - 62.63: 1787 62.63 - 93.94: 234 93.94 - 125.26: 28 125.26 - 156.57: 12 Dihedral angle restraints: 23724 sinusoidal: 12576 harmonic: 11148 Sorted by residual: dihedral pdb=" O4' U O 23 " pdb=" C1' U O 23 " pdb=" N1 U O 23 " pdb=" C2 U O 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.43 156.57 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U K 23 " pdb=" C1' U K 23 " pdb=" N1 U K 23 " pdb=" C2 U K 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.56 156.44 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U G 23 " pdb=" C1' U G 23 " pdb=" N1 U G 23 " pdb=" C2 U G 23 " ideal model delta sinusoidal sigma weight residual 200.00 43.56 156.44 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 23721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4457 0.049 - 0.098: 1163 0.098 - 0.147: 503 0.147 - 0.196: 122 0.196 - 0.245: 39 Chirality restraints: 6284 Sorted by residual: chirality pdb=" C3' U C 35 " pdb=" C4' U C 35 " pdb=" O3' U C 35 " pdb=" C2' U C 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C3' U G 35 " pdb=" C4' U G 35 " pdb=" O3' U G 35 " pdb=" C2' U G 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' U O 35 " pdb=" C4' U O 35 " pdb=" O3' U O 35 " pdb=" C2' U O 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.72 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 6281 not shown) Planarity restraints: 5620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 553 " 0.062 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO J 554 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO J 554 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 554 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 553 " -0.062 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO B 554 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 554 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 554 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 553 " -0.062 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO N 554 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO N 554 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO N 554 " -0.051 5.00e-02 4.00e+02 ... (remaining 5617 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 267 2.52 - 3.12: 26830 3.12 - 3.71: 58463 3.71 - 4.31: 81485 4.31 - 4.90: 130424 Nonbonded interactions: 297469 Sorted by model distance: nonbonded pdb=" OD1 ASP F 482 " pdb=" C2 U G 79 " model vdw 1.927 3.260 nonbonded pdb=" OD1 ASP N 482 " pdb=" C2 U O 79 " model vdw 1.928 3.260 nonbonded pdb=" OD1 ASP B 482 " pdb=" C2 U C 79 " model vdw 1.928 3.260 nonbonded pdb=" OD1 ASP J 482 " pdb=" C2 U K 79 " model vdw 1.930 3.260 nonbonded pdb=" OD1 ASP F 482 " pdb=" O2 U G 79 " model vdw 1.985 3.040 ... (remaining 297464 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' 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: 9.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.790 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 39068 Z= 0.415 Angle : 0.820 11.288 54132 Z= 0.528 Chirality : 0.057 0.245 6284 Planarity : 0.005 0.092 5620 Dihedral : 21.159 156.573 16484 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.00 % Allowed : 34.64 % Favored : 64.36 % 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: 1.08 (0.14), residues: 3688 helix: 1.57 (0.12), residues: 1852 sheet: 1.37 (0.22), residues: 568 loop : -0.87 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 664 TYR 0.030 0.002 TYR E 150 PHE 0.013 0.001 PHE B 727 TRP 0.011 0.002 TRP B 139 HIS 0.008 0.001 HIS M 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.41 (39068) covalent geometry : angle 0.81989 / 0.53 (54132) hydrogen bonds : bond 0.15535 / 10.53 ( 1772) hydrogen bonds : angle 6.34886 / 4.44 ( 4928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 1016 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 SER cc_start: 0.8151 (p) cc_final: 0.7780 (t) REVERT: A 114 ASN cc_start: 0.8327 (m-40) cc_final: 0.8088 (m110) REVERT: A 227 SER cc_start: 0.8666 (p) cc_final: 0.8413 (m) REVERT: B 392 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7642 (tt0) REVERT: B 405 LEU cc_start: 0.8815 (tt) cc_final: 0.8613 (tp) REVERT: B 406 PHE cc_start: 0.8638 (m-80) cc_final: 0.8378 (m-80) REVERT: B 509 MET cc_start: 0.7595 (mpm) cc_final: 0.7235 (mpt) REVERT: B 681 ASN cc_start: 0.8321 (m-40) cc_final: 0.7917 (m110) REVERT: B 730 ILE cc_start: 0.7736 (mt) cc_final: 0.7529 (mm) REVERT: B 738 SER cc_start: 0.8513 (t) cc_final: 0.8269 (m) REVERT: E 65 LEU cc_start: 0.7410 (tp) cc_final: 0.7206 (mm) REVERT: E 335 SER cc_start: 0.8078 (t) cc_final: 0.7716 (p) REVERT: F 134 ASP cc_start: 0.8126 (p0) cc_final: 0.7650 (p0) REVERT: F 402 GLU cc_start: 0.7382 (mp0) cc_final: 0.6828 (mp0) REVERT: F 473 MET cc_start: 0.7881 (ttp) cc_final: 0.7658 (mtm) REVERT: F 477 LEU cc_start: 0.8305 (mt) cc_final: 0.8063 (mp) REVERT: F 510 ASP cc_start: 0.8657 (m-30) cc_final: 0.8212 (m-30) REVERT: F 525 SER cc_start: 0.8027 (t) cc_final: 0.7734 (p) REVERT: F 535 ASN cc_start: 0.8446 (m110) cc_final: 0.8242 (m-40) REVERT: F 556 PHE cc_start: 0.8375 (t80) cc_final: 0.8161 (t80) REVERT: F 624 PHE cc_start: 0.8121 (t80) cc_final: 0.7910 (t80) REVERT: F 658 TYR cc_start: 0.8192 (m-80) cc_final: 0.7691 (m-80) REVERT: I 50 ILE cc_start: 0.8497 (mm) cc_final: 0.7900 (pp) REVERT: I 92 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7948 (mtmt) REVERT: I 139 LYS cc_start: 0.5626 (tmtt) cc_final: 0.4588 (mmpt) REVERT: I 255 LYS cc_start: 0.7229 (pttm) cc_final: 0.6979 (pttm) REVERT: I 276 LYS cc_start: 0.8479 (mttp) cc_final: 0.8265 (mmmm) REVERT: I 296 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7598 (mmtm) REVERT: J 97 TYR cc_start: 0.7858 (t80) cc_final: 0.7537 (t80) REVERT: J 289 VAL cc_start: 0.8784 (t) cc_final: 0.8554 (m) REVERT: J 358 LYS cc_start: 0.8368 (mttp) cc_final: 0.8159 (mttp) REVERT: J 367 LYS cc_start: 0.8854 (tttp) cc_final: 0.8552 (tttp) REVERT: J 398 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7095 (tm-30) REVERT: J 413 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7767 (t0) REVERT: J 438 TYR cc_start: 0.8496 (t80) cc_final: 0.8175 (t80) REVERT: J 466 LEU cc_start: 0.8298 (mt) cc_final: 0.8043 (mm) REVERT: J 469 LEU cc_start: 0.7841 (tp) cc_final: 0.7481 (tm) REVERT: J 494 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7331 (mm-30) REVERT: J 532 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7446 (ttm-80) REVERT: J 533 LYS cc_start: 0.8157 (mttm) cc_final: 0.7938 (mttt) REVERT: J 629 LYS cc_start: 0.8054 (pttt) cc_final: 0.7781 (pttp) REVERT: J 635 ASP cc_start: 0.6670 (p0) cc_final: 0.6363 (p0) REVERT: J 688 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7319 (tm-30) REVERT: J 735 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7410 (mm-30) REVERT: M 95 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7992 (tm-30) REVERT: M 181 ASP cc_start: 0.8131 (m-30) cc_final: 0.7876 (m-30) REVERT: M 276 LYS cc_start: 0.8285 (mttp) cc_final: 0.8032 (mttp) REVERT: N 1 MET cc_start: 0.6338 (mmt) cc_final: 0.6011 (mmt) REVERT: N 31 ARG cc_start: 0.8341 (mtp180) cc_final: 0.8098 (ttt180) REVERT: N 51 GLU cc_start: 0.7533 (mp0) cc_final: 0.7257 (mp0) REVERT: N 79 ILE cc_start: 0.8556 (tt) cc_final: 0.8348 (tp) REVERT: N 286 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7267 (mm-30) REVERT: N 307 TYR cc_start: 0.7485 (t80) cc_final: 0.6745 (t80) REVERT: N 308 SER cc_start: 0.7906 (m) cc_final: 0.7683 (p) REVERT: N 332 SER cc_start: 0.8302 (t) cc_final: 0.8089 (p) REVERT: N 371 THR cc_start: 0.8598 (m) cc_final: 0.8235 (p) REVERT: N 376 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7907 (ttt90) REVERT: N 382 SER cc_start: 0.8197 (p) cc_final: 0.7824 (t) REVERT: N 422 ASP cc_start: 0.7346 (t0) cc_final: 0.7037 (t0) REVERT: N 429 VAL cc_start: 0.7457 (m) cc_final: 0.7172 (p) REVERT: N 494 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7315 (mm-30) REVERT: N 509 MET cc_start: 0.7010 (mpm) cc_final: 0.6530 (mpt) REVERT: N 532 ARG cc_start: 0.7189 (tpp80) cc_final: 0.6904 (tpp80) REVERT: N 537 TYR cc_start: 0.8346 (t80) cc_final: 0.7686 (t80) REVERT: N 547 LEU cc_start: 0.8681 (mt) cc_final: 0.8445 (mt) REVERT: N 550 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7226 (mt-10) REVERT: N 639 GLU cc_start: 0.6678 (tt0) cc_final: 0.6423 (tt0) REVERT: N 650 PHE cc_start: 0.8569 (m-80) cc_final: 0.8231 (m-80) REVERT: N 662 LYS cc_start: 0.8043 (tttm) cc_final: 0.7843 (mtpp) REVERT: N 679 TYR cc_start: 0.7755 (m-80) cc_final: 0.7217 (m-10) REVERT: N 735 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7290 (mm-30) outliers start: 35 outliers final: 14 residues processed: 1030 average time/residue: 0.7165 time to fit residues: 898.0867 Evaluate side-chains 910 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 894 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain I residue 248 ASN Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 670 GLU Chi-restraints excluded: chain J residue 685 PHE Chi-restraints excluded: chain N residue 474 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 overall best weight: 0.2674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 185 GLN A 254 ASN A 279 HIS A 364 HIS B 38 ASN B 259 ASN B 433 ASN B 528 ASN B 703 ASN B 721 GLN E 185 GLN E 235 GLN E 254 ASN E 279 HIS E 363 ASN F 33 ASN F 38 ASN F 413 ASN F 508 HIS ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 ASN F 682 ASN F 721 GLN I 232 ASN ** I 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 ASN J 38 ASN J 52 ASN J 384 ASN J 433 ASN J 502 GLN J 558 ASN J 721 GLN M 185 GLN M 254 ASN M 284 ASN M 353 GLN M 364 HIS N 38 ASN N 328 ASN N 379 ASN N 384 ASN N 433 ASN N 502 GLN N 508 HIS N 558 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.164409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127671 restraints weight = 54622.673| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.81 r_work: 0.3437 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39068 Z= 0.150 Angle : 0.623 9.923 54132 Z= 0.350 Chirality : 0.046 0.324 6284 Planarity : 0.004 0.044 5620 Dihedral : 19.649 152.989 8753 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.72 % Allowed : 29.61 % Favored : 65.68 % 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: 1.25 (0.14), residues: 3688 helix: 1.78 (0.12), residues: 1900 sheet: 1.38 (0.22), residues: 560 loop : -0.98 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 467 TYR 0.018 0.001 TYR M 318 PHE 0.016 0.001 PHE F 727 TRP 0.006 0.001 TRP J 139 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (39068) covalent geometry : angle 0.62284 / 0.35 (54132) hydrogen bonds : bond 0.05482 / 3.58 ( 1772) hydrogen bonds : angle 4.23937 / 3.00 ( 4928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 924 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8279 (mtmt) REVERT: A 109 SER cc_start: 0.8221 (p) cc_final: 0.7836 (t) REVERT: A 110 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7678 (m) REVERT: A 114 ASN cc_start: 0.8406 (m-40) cc_final: 0.8186 (m110) REVERT: A 227 SER cc_start: 0.8578 (p) cc_final: 0.8321 (m) REVERT: A 254 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 342 GLU cc_start: 0.7929 (tt0) cc_final: 0.7441 (tt0) REVERT: B 162 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7257 (tpp80) REVERT: B 392 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8097 (tt0) REVERT: B 405 LEU cc_start: 0.8817 (tt) cc_final: 0.8617 (tp) REVERT: B 406 PHE cc_start: 0.8548 (m-80) cc_final: 0.8306 (m-80) REVERT: B 425 ASP cc_start: 0.7844 (t0) cc_final: 0.7553 (t70) REVERT: B 461 THR cc_start: 0.8564 (p) cc_final: 0.8269 (t) REVERT: B 467 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7339 (mmm-85) REVERT: B 476 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: B 658 TYR cc_start: 0.8404 (m-80) cc_final: 0.8161 (m-80) REVERT: B 662 LYS cc_start: 0.7698 (tttm) cc_final: 0.7434 (tptm) REVERT: B 674 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 677 LYS cc_start: 0.8588 (tptp) cc_final: 0.7983 (tptp) REVERT: B 681 ASN cc_start: 0.8441 (m-40) cc_final: 0.7896 (m110) REVERT: B 710 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 738 SER cc_start: 0.8565 (t) cc_final: 0.8334 (m) REVERT: E 65 LEU cc_start: 0.7587 (tp) cc_final: 0.7355 (mm) REVERT: E 129 LYS cc_start: 0.7125 (pttt) cc_final: 0.6621 (tttm) REVERT: E 139 LYS cc_start: 0.5224 (tptt) cc_final: 0.3943 (mmmt) REVERT: E 236 SER cc_start: 0.8457 (t) cc_final: 0.8097 (p) REVERT: E 276 LYS cc_start: 0.8443 (mttp) cc_final: 0.8219 (mttm) REVERT: E 338 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8066 (mttt) REVERT: E 357 ILE cc_start: 0.8302 (mp) cc_final: 0.7978 (tt) REVERT: F 413 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8158 (t0) REVERT: F 464 PHE cc_start: 0.7834 (m-80) cc_final: 0.7576 (m-10) REVERT: F 510 ASP cc_start: 0.8489 (m-30) cc_final: 0.8162 (m-30) REVERT: F 525 SER cc_start: 0.8142 (t) cc_final: 0.7851 (p) REVERT: F 582 MET cc_start: 0.7470 (mmp) cc_final: 0.7257 (mmp) REVERT: F 624 PHE cc_start: 0.8144 (t80) cc_final: 0.7928 (t80) REVERT: F 626 ASN cc_start: 0.8234 (m-40) cc_final: 0.7859 (m-40) REVERT: F 650 PHE cc_start: 0.8511 (m-80) cc_final: 0.8283 (m-80) REVERT: F 658 TYR cc_start: 0.8339 (m-80) cc_final: 0.8086 (m-80) REVERT: I 49 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7869 (mtmt) REVERT: I 65 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7694 (mm) REVERT: I 110 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6913 (p) REVERT: I 139 LYS cc_start: 0.5742 (tmtt) cc_final: 0.4683 (mmpt) REVERT: I 255 LYS cc_start: 0.7772 (pttm) cc_final: 0.7496 (pttm) REVERT: I 276 LYS cc_start: 0.8632 (mttp) cc_final: 0.8429 (mmmm) REVERT: J 54 LYS cc_start: 0.8476 (mttt) cc_final: 0.8270 (mmtm) REVERT: J 97 TYR cc_start: 0.7879 (t80) cc_final: 0.7563 (t80) REVERT: J 288 GLU cc_start: 0.7908 (pm20) cc_final: 0.7384 (pm20) REVERT: J 344 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: J 413 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (t0) REVERT: J 452 ASP cc_start: 0.8286 (t70) cc_final: 0.8027 (t0) REVERT: J 494 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7368 (mm-30) REVERT: J 568 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.3534 (mmp) REVERT: J 629 LYS cc_start: 0.8177 (pttt) cc_final: 0.7878 (pttp) REVERT: J 681 ASN cc_start: 0.8160 (t0) cc_final: 0.7944 (m-40) REVERT: J 688 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7632 (tm-30) REVERT: J 735 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7892 (mm-30) REVERT: M 95 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8099 (tm-30) REVERT: M 216 ASP cc_start: 0.7743 (m-30) cc_final: 0.7390 (m-30) REVERT: M 276 LYS cc_start: 0.8389 (mttp) cc_final: 0.8084 (mttp) REVERT: M 285 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8134 (mm) REVERT: M 289 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.7019 (p0) REVERT: M 335 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8250 (p) REVERT: M 364 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8252 (m170) REVERT: N 1 MET cc_start: 0.6846 (mmt) cc_final: 0.6386 (mmt) REVERT: N 17 VAL cc_start: 0.8629 (t) cc_final: 0.8284 (p) REVERT: N 18 ILE cc_start: 0.8711 (tt) cc_final: 0.8452 (pt) REVERT: N 47 TYR cc_start: 0.8723 (m-80) cc_final: 0.8508 (m-80) REVERT: N 50 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8217 (OUTLIER) REVERT: N 51 GLU cc_start: 0.7742 (mp0) cc_final: 0.7540 (mp0) REVERT: N 146 VAL cc_start: 0.8151 (p) cc_final: 0.7898 (m) REVERT: N 286 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: N 308 SER cc_start: 0.8356 (m) cc_final: 0.8056 (t) REVERT: N 344 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8485 (mmmm) REVERT: N 376 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8232 (ttt90) REVERT: N 422 ASP cc_start: 0.7345 (t0) cc_final: 0.7138 (t0) REVERT: N 429 VAL cc_start: 0.7845 (m) cc_final: 0.7589 (p) REVERT: N 464 PHE cc_start: 0.7721 (m-80) cc_final: 0.7510 (m-10) REVERT: N 476 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: N 494 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7259 (mm-30) REVERT: N 497 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7813 (tt) REVERT: N 509 MET cc_start: 0.7610 (mpm) cc_final: 0.7206 (mpt) REVERT: N 532 ARG cc_start: 0.8035 (tpp80) cc_final: 0.7763 (tpp80) REVERT: N 537 TYR cc_start: 0.8499 (t80) cc_final: 0.7887 (t80) REVERT: N 547 LEU cc_start: 0.8735 (mt) cc_final: 0.8457 (mt) REVERT: N 550 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7641 (mt-10) REVERT: N 585 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6267 (ttp-110) REVERT: N 586 TYR cc_start: 0.7801 (m-10) cc_final: 0.7317 (m-10) REVERT: N 627 TYR cc_start: 0.8070 (t80) cc_final: 0.7867 (t80) REVERT: N 631 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.7516 (tmtm) REVERT: N 635 ASP cc_start: 0.7121 (p0) cc_final: 0.6695 (p0) REVERT: N 639 GLU cc_start: 0.6821 (tt0) cc_final: 0.6554 (tt0) REVERT: N 650 PHE cc_start: 0.8650 (m-80) cc_final: 0.8404 (m-80) REVERT: N 735 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7767 (mm-30) REVERT: N 745 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6630 (tm-30) REVERT: N 747 SER cc_start: 0.8049 (p) cc_final: 0.7731 (p) outliers start: 165 outliers final: 54 residues processed: 1014 average time/residue: 0.6923 time to fit residues: 858.2017 Evaluate side-chains 960 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 885 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 710 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 335 SER Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain J residue 305 LYS Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 383 ASP Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 476 GLU Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 560 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 710 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 233 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 335 SER Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 364 HIS Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 344 LYS Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 433 ASN Chi-restraints excluded: chain N residue 476 GLU Chi-restraints excluded: chain N residue 497 LEU Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 631 LYS Chi-restraints excluded: chain N residue 672 PHE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 710 THR Chi-restraints excluded: chain N residue 731 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 24 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 362 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 6 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 254 ASN A 353 GLN B 65 ASN B 528 ASN B 703 ASN E 185 GLN F 65 ASN F 502 GLN F 508 HIS F 535 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 ASN I 353 GLN J 52 ASN J 259 ASN M 254 ASN M 284 ASN N 379 ASN N 433 ASN N 502 GLN N 558 ASN N 682 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124680 restraints weight = 54230.185| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.80 r_work: 0.3394 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39068 Z= 0.139 Angle : 0.554 7.913 54132 Z= 0.318 Chirality : 0.043 0.255 6284 Planarity : 0.004 0.040 5620 Dihedral : 19.404 149.552 8722 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.03 % Allowed : 29.12 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.14), residues: 3688 helix: 1.87 (0.12), residues: 1908 sheet: 1.23 (0.22), residues: 576 loop : -0.92 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 673 TYR 0.022 0.001 TYR M 318 PHE 0.014 0.001 PHE F 727 TRP 0.009 0.001 TRP B 697 HIS 0.017 0.001 HIS M 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (39068) covalent geometry : angle 0.55374 / 0.32 (54132) hydrogen bonds : bond 0.04889 / 3.20 ( 1772) hydrogen bonds : angle 4.06002 / 2.87 ( 4928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 892 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8272 (mtmt) REVERT: A 110 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7638 (m) REVERT: A 161 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7517 (tt) REVERT: A 227 SER cc_start: 0.8638 (p) cc_final: 0.8376 (m) REVERT: A 342 GLU cc_start: 0.7955 (tt0) cc_final: 0.7435 (tt0) REVERT: B 134 ASP cc_start: 0.7795 (p0) cc_final: 0.7552 (p0) REVERT: B 162 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7389 (tpp80) REVERT: B 375 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7357 (pm20) REVERT: B 406 PHE cc_start: 0.8573 (m-80) cc_final: 0.8292 (m-80) REVERT: B 425 ASP cc_start: 0.7877 (t0) cc_final: 0.7600 (t70) REVERT: B 440 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7701 (ptmm) REVERT: B 460 LYS cc_start: 0.8447 (mppt) cc_final: 0.8136 (mppt) REVERT: B 461 THR cc_start: 0.8556 (p) cc_final: 0.8297 (t) REVERT: B 497 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7107 (tt) REVERT: B 501 ILE cc_start: 0.8602 (mm) cc_final: 0.8386 (mm) REVERT: B 641 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7010 (mt-10) REVERT: B 662 LYS cc_start: 0.7726 (tttm) cc_final: 0.7396 (tptm) REVERT: B 677 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7970 (tptp) REVERT: B 681 ASN cc_start: 0.8425 (m-40) cc_final: 0.7842 (m110) REVERT: B 738 SER cc_start: 0.8555 (t) cc_final: 0.8331 (m) REVERT: E 129 LYS cc_start: 0.7186 (pttt) cc_final: 0.6560 (ttmm) REVERT: E 139 LYS cc_start: 0.5150 (tptt) cc_final: 0.4874 (mmmt) REVERT: E 265 ARG cc_start: 0.8437 (ptt-90) cc_final: 0.8070 (ptt180) REVERT: E 357 ILE cc_start: 0.8305 (mp) cc_final: 0.7951 (tt) REVERT: F 51 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: F 78 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7155 (tmt-80) REVERT: F 510 ASP cc_start: 0.8583 (m-30) cc_final: 0.8186 (m-30) REVERT: F 525 SER cc_start: 0.8171 (t) cc_final: 0.7867 (p) REVERT: F 562 ASP cc_start: 0.6914 (m-30) cc_final: 0.6601 (m-30) REVERT: F 582 MET cc_start: 0.7526 (mmp) cc_final: 0.7289 (mmp) REVERT: F 658 TYR cc_start: 0.8463 (m-80) cc_final: 0.8164 (m-80) REVERT: F 675 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8071 (ttmm) REVERT: F 677 LYS cc_start: 0.9054 (tppp) cc_final: 0.8791 (ttmm) REVERT: F 723 LEU cc_start: 0.8592 (mm) cc_final: 0.8316 (mt) REVERT: I 49 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7833 (mtmt) REVERT: I 65 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7753 (mm) REVERT: I 110 SER cc_start: 0.7282 (OUTLIER) cc_final: 0.6936 (p) REVERT: I 139 LYS cc_start: 0.5859 (tmtt) cc_final: 0.4788 (mmpt) REVERT: I 191 LYS cc_start: 0.8295 (tppt) cc_final: 0.8039 (mmtm) REVERT: I 255 LYS cc_start: 0.7812 (pttm) cc_final: 0.7526 (pttm) REVERT: J 51 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: J 54 LYS cc_start: 0.8540 (mttt) cc_final: 0.8309 (mmtt) REVERT: J 97 TYR cc_start: 0.7954 (t80) cc_final: 0.7610 (t80) REVERT: J 285 ASP cc_start: 0.7798 (t0) cc_final: 0.7576 (t70) REVERT: J 344 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8338 (mtpt) REVERT: J 398 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7651 (tm-30) REVERT: J 404 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7220 (tt0) REVERT: J 413 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8158 (t0) REVERT: J 472 LYS cc_start: 0.8538 (tttt) cc_final: 0.8304 (ttmm) REVERT: J 494 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7446 (mm-30) REVERT: J 526 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8439 (mtm180) REVERT: J 529 LYS cc_start: 0.8278 (ttmm) cc_final: 0.8049 (ttmm) REVERT: J 532 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7938 (ttm-80) REVERT: J 568 MET cc_start: 0.4884 (OUTLIER) cc_final: 0.3822 (mmp) REVERT: J 629 LYS cc_start: 0.8167 (pttt) cc_final: 0.7890 (pttp) REVERT: J 681 ASN cc_start: 0.8198 (t0) cc_final: 0.7984 (m-40) REVERT: J 688 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7594 (tm-30) REVERT: J 735 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7889 (mm-30) REVERT: M 91 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8520 (mt) REVERT: M 95 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8094 (tm-30) REVERT: M 121 LYS cc_start: 0.8276 (ttmt) cc_final: 0.8060 (ttmt) REVERT: M 181 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: M 227 SER cc_start: 0.8342 (p) cc_final: 0.8031 (m) REVERT: M 269 SER cc_start: 0.8437 (m) cc_final: 0.8101 (t) REVERT: M 276 LYS cc_start: 0.8386 (mttp) cc_final: 0.8098 (mttp) REVERT: N 50 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8391 (OUTLIER) REVERT: N 122 LYS cc_start: 0.7843 (mtmm) cc_final: 0.7518 (mtpp) REVERT: N 286 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: N 302 ASN cc_start: 0.7539 (m-40) cc_final: 0.7274 (m-40) REVERT: N 308 SER cc_start: 0.8451 (m) cc_final: 0.8130 (t) REVERT: N 344 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (mttt) REVERT: N 376 ARG cc_start: 0.8560 (ttt90) cc_final: 0.8230 (ttt90) REVERT: N 402 GLU cc_start: 0.7247 (mp0) cc_final: 0.6915 (mp0) REVERT: N 413 ASN cc_start: 0.8230 (t0) cc_final: 0.7970 (t0) REVERT: N 422 ASP cc_start: 0.7387 (t0) cc_final: 0.7174 (t0) REVERT: N 494 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7266 (mm-30) REVERT: N 509 MET cc_start: 0.7717 (mpm) cc_final: 0.7374 (mpt) REVERT: N 532 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7799 (tpp80) REVERT: N 547 LEU cc_start: 0.8714 (mt) cc_final: 0.8483 (mt) REVERT: N 550 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7629 (mt-10) REVERT: N 558 ASN cc_start: 0.7887 (m110) cc_final: 0.7668 (m-40) REVERT: N 582 MET cc_start: 0.6829 (mmp) cc_final: 0.6539 (mmp) REVERT: N 631 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7625 (tptm) REVERT: N 635 ASP cc_start: 0.7108 (p0) cc_final: 0.6505 (p0) REVERT: N 639 GLU cc_start: 0.6882 (tt0) cc_final: 0.6513 (tt0) REVERT: N 650 PHE cc_start: 0.8666 (m-80) cc_final: 0.8409 (m-80) REVERT: N 679 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: N 685 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.6060 (t80) REVERT: N 735 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7793 (mm-30) REVERT: N 745 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6704 (tm-30) outliers start: 176 outliers final: 67 residues processed: 975 average time/residue: 0.6566 time to fit residues: 786.4848 Evaluate side-chains 980 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 891 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 508 HIS Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 233 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 344 LYS Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 462 GLU Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 631 LYS Chi-restraints excluded: chain N residue 672 PHE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 685 PHE Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 731 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 301 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 chunk 339 optimal weight: 0.3980 chunk 199 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 114 ASN A 279 HIS A 353 GLN B 65 ASN B 433 ASN B 528 ASN B 558 ASN B 703 ASN E 185 GLN F 33 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 ASN I 353 GLN J 52 ASN M 38 ASN M 284 ASN M 353 GLN N 379 ASN N 433 ASN N 502 GLN N 721 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.158149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120322 restraints weight = 53540.793| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.89 r_work: 0.3322 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 39068 Z= 0.196 Angle : 0.596 8.497 54132 Z= 0.339 Chirality : 0.045 0.266 6284 Planarity : 0.004 0.043 5620 Dihedral : 19.334 152.031 8722 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.32 % Allowed : 28.69 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3688 helix: 1.80 (0.12), residues: 1908 sheet: 0.98 (0.22), residues: 576 loop : -0.95 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 20 TYR 0.027 0.002 TYR J 627 PHE 0.022 0.002 PHE B 299 TRP 0.012 0.002 TRP J 139 HIS 0.052 0.002 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (39068) covalent geometry : angle 0.59607 / 0.34 (54132) hydrogen bonds : bond 0.05519 / 3.59 ( 1772) hydrogen bonds : angle 4.07758 / 2.88 ( 4928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 915 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6787 (OUTLIER) cc_final: 0.6292 (p0) REVERT: A 241 ARG cc_start: 0.8453 (ttt-90) cc_final: 0.8174 (ttt-90) REVERT: A 342 GLU cc_start: 0.7931 (tt0) cc_final: 0.7592 (tt0) REVERT: B 143 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7188 (t70) REVERT: B 162 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7494 (tpp80) REVERT: B 375 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: B 425 ASP cc_start: 0.7914 (t0) cc_final: 0.7675 (t70) REVERT: B 459 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 461 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 472 LYS cc_start: 0.8460 (tptt) cc_final: 0.8056 (tppt) REVERT: B 482 ASP cc_start: 0.7448 (m-30) cc_final: 0.7136 (m-30) REVERT: B 484 TYR cc_start: 0.6581 (m-80) cc_final: 0.6105 (m-80) REVERT: B 497 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7114 (tt) REVERT: B 532 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7287 (ttp80) REVERT: B 582 MET cc_start: 0.7234 (mmp) cc_final: 0.6667 (mmp) REVERT: B 641 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6925 (mt-10) REVERT: B 677 LYS cc_start: 0.8658 (tptp) cc_final: 0.7987 (tptp) REVERT: B 681 ASN cc_start: 0.8480 (m-40) cc_final: 0.7978 (m110) REVERT: B 708 LYS cc_start: 0.8253 (tttp) cc_final: 0.7944 (ttpp) REVERT: B 738 SER cc_start: 0.8621 (t) cc_final: 0.8353 (m) REVERT: B 745 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7070 (tm-30) REVERT: E 129 LYS cc_start: 0.7210 (pttt) cc_final: 0.6604 (mtmt) REVERT: E 265 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.8158 (ptt90) REVERT: E 342 GLU cc_start: 0.7649 (tt0) cc_final: 0.7362 (tt0) REVERT: F 51 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: F 78 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7282 (tmt-80) REVERT: F 276 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: F 385 GLU cc_start: 0.8349 (mp0) cc_final: 0.7908 (mp0) REVERT: F 510 ASP cc_start: 0.8760 (m-30) cc_final: 0.8244 (m-30) REVERT: F 525 SER cc_start: 0.8281 (t) cc_final: 0.7958 (p) REVERT: F 556 PHE cc_start: 0.8649 (t80) cc_final: 0.8254 (t80) REVERT: F 562 ASP cc_start: 0.7158 (m-30) cc_final: 0.6794 (m-30) REVERT: F 582 MET cc_start: 0.7577 (mmp) cc_final: 0.7318 (mmp) REVERT: F 650 PHE cc_start: 0.8641 (m-80) cc_final: 0.8415 (m-80) REVERT: F 675 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8140 (ttmm) REVERT: F 677 LYS cc_start: 0.9059 (tppp) cc_final: 0.8827 (ttmm) REVERT: F 723 LEU cc_start: 0.8636 (mm) cc_final: 0.8389 (mt) REVERT: I 51 PHE cc_start: 0.7956 (m-10) cc_final: 0.7750 (m-10) REVERT: I 65 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7798 (mm) REVERT: I 67 LEU cc_start: 0.7925 (mt) cc_final: 0.7595 (mp) REVERT: I 110 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.7014 (p) REVERT: I 139 LYS cc_start: 0.5902 (tmtt) cc_final: 0.4782 (mmpt) REVERT: I 191 LYS cc_start: 0.8438 (tppt) cc_final: 0.8205 (mmtm) REVERT: I 219 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7834 (mt) REVERT: I 237 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7998 (mtpt) REVERT: I 255 LYS cc_start: 0.7865 (pttm) cc_final: 0.7620 (pttm) REVERT: I 269 SER cc_start: 0.8375 (m) cc_final: 0.8081 (t) REVERT: J 51 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: J 54 LYS cc_start: 0.8624 (mttt) cc_final: 0.8419 (mmtt) REVERT: J 55 VAL cc_start: 0.8869 (p) cc_final: 0.8608 (m) REVERT: J 97 TYR cc_start: 0.8132 (t80) cc_final: 0.7817 (t80) REVERT: J 285 ASP cc_start: 0.7859 (t0) cc_final: 0.7632 (t70) REVERT: J 344 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8355 (mtmt) REVERT: J 404 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7240 (tt0) REVERT: J 413 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8169 (t160) REVERT: J 472 LYS cc_start: 0.8553 (tttt) cc_final: 0.8298 (ttmm) REVERT: J 494 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7401 (mm-30) REVERT: J 529 LYS cc_start: 0.8308 (ttmm) cc_final: 0.8036 (ttmm) REVERT: J 532 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7961 (ttm-80) REVERT: J 568 MET cc_start: 0.5078 (OUTLIER) cc_final: 0.4024 (mmp) REVERT: J 597 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8108 (ttpp) REVERT: J 629 LYS cc_start: 0.8209 (pttt) cc_final: 0.7967 (pttp) REVERT: J 631 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7443 (tppt) REVERT: J 635 ASP cc_start: 0.6628 (p0) cc_final: 0.6089 (p0) REVERT: J 675 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7977 (ttpt) REVERT: J 681 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: J 688 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7615 (tm-30) REVERT: J 735 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7936 (mm-30) REVERT: M 44 ILE cc_start: 0.8288 (mp) cc_final: 0.8085 (mm) REVERT: M 160 MET cc_start: 0.7251 (tpp) cc_final: 0.6980 (tpp) REVERT: M 167 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7536 (mtm110) REVERT: M 180 MET cc_start: 0.8330 (mmm) cc_final: 0.8077 (tpp) REVERT: M 181 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: M 227 SER cc_start: 0.8416 (p) cc_final: 0.8139 (m) REVERT: M 269 SER cc_start: 0.8527 (m) cc_final: 0.8216 (t) REVERT: M 276 LYS cc_start: 0.8471 (mttp) cc_final: 0.8204 (mttm) REVERT: N 122 LYS cc_start: 0.7831 (mtmm) cc_final: 0.7510 (mtpp) REVERT: N 286 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: N 302 ASN cc_start: 0.7903 (m-40) cc_final: 0.7655 (m-40) REVERT: N 308 SER cc_start: 0.8591 (m) cc_final: 0.8289 (t) REVERT: N 344 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (mttt) REVERT: N 376 ARG cc_start: 0.8542 (ttt90) cc_final: 0.8236 (ttt90) REVERT: N 422 ASP cc_start: 0.7404 (t0) cc_final: 0.7201 (t0) REVERT: N 483 TYR cc_start: 0.7670 (p90) cc_final: 0.7362 (p90) REVERT: N 494 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7273 (mm-30) REVERT: N 509 MET cc_start: 0.7860 (mpm) cc_final: 0.7650 (mpm) REVERT: N 522 ASN cc_start: 0.7700 (p0) cc_final: 0.7362 (p0) REVERT: N 526 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8420 (ptm-80) REVERT: N 532 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7767 (tpp80) REVERT: N 547 LEU cc_start: 0.8745 (mt) cc_final: 0.8495 (mt) REVERT: N 550 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7634 (mt-10) REVERT: N 558 ASN cc_start: 0.7928 (m110) cc_final: 0.7653 (m-40) REVERT: N 582 MET cc_start: 0.6885 (mmp) cc_final: 0.6671 (mmp) REVERT: N 631 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7996 (tptm) REVERT: N 639 GLU cc_start: 0.6929 (tt0) cc_final: 0.6552 (tt0) REVERT: N 650 PHE cc_start: 0.8725 (m-80) cc_final: 0.8395 (m-80) REVERT: N 655 GLU cc_start: 0.8179 (tt0) cc_final: 0.7951 (tp30) REVERT: N 679 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7787 (m-10) REVERT: N 735 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7841 (mm-30) REVERT: N 745 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6662 (tm-30) outliers start: 186 outliers final: 90 residues processed: 1000 average time/residue: 0.6710 time to fit residues: 823.6479 Evaluate side-chains 1009 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 895 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 560 ILE Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 560 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 670 GLU Chi-restraints excluded: chain J residue 675 LYS Chi-restraints excluded: chain J residue 681 ASN Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 710 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 233 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 270 LYS Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 344 LYS Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 474 ILE Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 631 LYS Chi-restraints excluded: chain N residue 648 LEU Chi-restraints excluded: chain N residue 672 PHE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 196 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 290 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 185 GLN B 65 ASN B 433 ASN B 528 ASN B 703 ASN E 185 GLN F 33 ASN F 502 GLN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 ASN I 232 ASN I 235 GLN J 52 ASN M 38 ASN M 284 ASN M 362 GLN N 379 ASN N 413 ASN N 433 ASN N 558 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.155038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117492 restraints weight = 53429.793| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.81 r_work: 0.3283 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 39068 Z= 0.254 Angle : 0.635 11.430 54132 Z= 0.361 Chirality : 0.047 0.257 6284 Planarity : 0.005 0.053 5620 Dihedral : 19.352 159.074 8720 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.69 % Allowed : 28.52 % Favored : 65.79 % 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: 0.86 (0.14), residues: 3688 helix: 1.61 (0.12), residues: 1900 sheet: 0.71 (0.22), residues: 576 loop : -1.18 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 718 TYR 0.029 0.002 TYR A 150 PHE 0.027 0.002 PHE M 339 TRP 0.017 0.003 TRP J 139 HIS 0.012 0.002 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (39068) covalent geometry : angle 0.63513 / 0.36 (54132) hydrogen bonds : bond 0.06203 / 4.08 ( 1772) hydrogen bonds : angle 4.22055 / 2.98 ( 4928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 941 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6494 (p0) REVERT: A 89 SER cc_start: 0.8029 (t) cc_final: 0.7783 (m) REVERT: A 92 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8260 (mtmt) REVERT: A 109 SER cc_start: 0.8246 (p) cc_final: 0.8022 (t) REVERT: A 181 ASP cc_start: 0.8361 (m-30) cc_final: 0.7750 (m-30) REVERT: A 285 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 93 HIS cc_start: 0.8465 (m90) cc_final: 0.8188 (m90) REVERT: B 143 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7212 (t70) REVERT: B 162 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7627 (tpp80) REVERT: B 375 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7428 (pm20) REVERT: B 440 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7863 (ptmm) REVERT: B 472 LYS cc_start: 0.8502 (tptt) cc_final: 0.8105 (tppt) REVERT: B 482 ASP cc_start: 0.7572 (m-30) cc_final: 0.7196 (m-30) REVERT: B 497 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7296 (tt) REVERT: B 532 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7360 (ttp80) REVERT: B 582 MET cc_start: 0.7149 (mmp) cc_final: 0.6558 (mmp) REVERT: B 641 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6917 (mt-10) REVERT: B 677 LYS cc_start: 0.8689 (tptp) cc_final: 0.8011 (tptp) REVERT: B 681 ASN cc_start: 0.8531 (m-40) cc_final: 0.8026 (m110) REVERT: B 708 LYS cc_start: 0.8436 (tttp) cc_final: 0.8147 (ttpp) REVERT: B 738 SER cc_start: 0.8561 (t) cc_final: 0.8269 (m) REVERT: B 745 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: E 129 LYS cc_start: 0.7203 (pttt) cc_final: 0.6551 (mtmt) REVERT: E 336 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (mp) REVERT: F 78 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7297 (tmt-80) REVERT: F 276 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7012 (pt0) REVERT: F 305 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8056 (mppt) REVERT: F 385 GLU cc_start: 0.8372 (mp0) cc_final: 0.7918 (mp0) REVERT: F 477 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8274 (mt) REVERT: F 510 ASP cc_start: 0.8737 (m-30) cc_final: 0.8271 (m-30) REVERT: F 525 SER cc_start: 0.8312 (t) cc_final: 0.7984 (p) REVERT: F 556 PHE cc_start: 0.8690 (t80) cc_final: 0.8271 (t80) REVERT: F 562 ASP cc_start: 0.7273 (m-30) cc_final: 0.6810 (m-30) REVERT: F 582 MET cc_start: 0.7563 (mmp) cc_final: 0.7293 (mmp) REVERT: F 629 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8261 (tppt) REVERT: F 677 LYS cc_start: 0.9036 (tppp) cc_final: 0.8778 (ttmm) REVERT: F 723 LEU cc_start: 0.8711 (mm) cc_final: 0.8448 (mt) REVERT: I 39 LYS cc_start: 0.8373 (tttt) cc_final: 0.8168 (pttt) REVERT: I 65 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7851 (mm) REVERT: I 67 LEU cc_start: 0.7943 (mt) cc_final: 0.7600 (mp) REVERT: I 110 SER cc_start: 0.7450 (OUTLIER) cc_final: 0.7112 (p) REVERT: I 139 LYS cc_start: 0.5723 (tmtt) cc_final: 0.4630 (mmpt) REVERT: I 219 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7940 (mt) REVERT: I 269 SER cc_start: 0.8402 (m) cc_final: 0.8147 (t) REVERT: I 360 ASP cc_start: 0.7867 (t0) cc_final: 0.7610 (t0) REVERT: J 54 LYS cc_start: 0.8617 (mttt) cc_final: 0.8345 (mmtt) REVERT: J 55 VAL cc_start: 0.8858 (p) cc_final: 0.8622 (m) REVERT: J 97 TYR cc_start: 0.8273 (t80) cc_final: 0.7905 (t80) REVERT: J 344 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8413 (mtpp) REVERT: J 413 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8183 (t160) REVERT: J 472 LYS cc_start: 0.8549 (tttt) cc_final: 0.8262 (ttmm) REVERT: J 494 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7336 (mm-30) REVERT: J 529 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7999 (ttmm) REVERT: J 532 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7969 (ttm-80) REVERT: J 562 ASP cc_start: 0.6833 (m-30) cc_final: 0.6473 (m-30) REVERT: J 568 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4103 (mmp) REVERT: J 597 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8142 (ttpp) REVERT: J 629 LYS cc_start: 0.8153 (pttt) cc_final: 0.7871 (pttp) REVERT: J 631 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7680 (ttmm) REVERT: J 635 ASP cc_start: 0.6613 (p0) cc_final: 0.6366 (p0) REVERT: J 639 GLU cc_start: 0.6796 (tt0) cc_final: 0.6578 (tt0) REVERT: J 674 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7497 (mm-30) REVERT: J 675 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7978 (ttpt) REVERT: J 681 ASN cc_start: 0.8153 (t0) cc_final: 0.7948 (m-40) REVERT: J 688 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7619 (tm-30) REVERT: M 44 ILE cc_start: 0.8295 (mp) cc_final: 0.8088 (mm) REVERT: M 91 LEU cc_start: 0.8847 (mm) cc_final: 0.8606 (mt) REVERT: M 160 MET cc_start: 0.7192 (tpp) cc_final: 0.6889 (tpp) REVERT: M 180 MET cc_start: 0.8361 (mmm) cc_final: 0.8116 (tpp) REVERT: M 181 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: M 210 SER cc_start: 0.8111 (m) cc_final: 0.7908 (t) REVERT: M 211 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8064 (mmmm) REVERT: M 227 SER cc_start: 0.8472 (p) cc_final: 0.8243 (m) REVERT: M 269 SER cc_start: 0.8628 (m) cc_final: 0.8318 (t) REVERT: M 276 LYS cc_start: 0.8471 (mttp) cc_final: 0.8206 (mttm) REVERT: M 337 VAL cc_start: 0.8582 (t) cc_final: 0.8212 (m) REVERT: M 344 LYS cc_start: 0.8244 (mmmm) cc_final: 0.8009 (mmmm) REVERT: N 122 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7519 (mtmm) REVERT: N 286 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: N 302 ASN cc_start: 0.8090 (m-40) cc_final: 0.7838 (m-40) REVERT: N 308 SER cc_start: 0.8635 (m) cc_final: 0.8342 (t) REVERT: N 344 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8480 (mmmm) REVERT: N 376 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8237 (ttt90) REVERT: N 414 LEU cc_start: 0.8389 (mt) cc_final: 0.8125 (mp) REVERT: N 494 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7297 (mm-30) REVERT: N 502 GLN cc_start: 0.7468 (tm-30) cc_final: 0.7209 (tp-100) REVERT: N 509 MET cc_start: 0.7896 (mpm) cc_final: 0.7674 (mpt) REVERT: N 526 ARG cc_start: 0.8741 (ptm-80) cc_final: 0.8509 (ptm-80) REVERT: N 532 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7643 (tpp80) REVERT: N 534 LEU cc_start: 0.8964 (mt) cc_final: 0.8734 (mp) REVERT: N 547 LEU cc_start: 0.8736 (mt) cc_final: 0.8516 (mt) REVERT: N 550 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7491 (mt-10) REVERT: N 558 ASN cc_start: 0.7985 (m-40) cc_final: 0.7600 (m-40) REVERT: N 639 GLU cc_start: 0.6878 (tt0) cc_final: 0.6413 (tt0) REVERT: N 656 THR cc_start: 0.8874 (m) cc_final: 0.8594 (p) REVERT: N 679 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: N 735 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7837 (mm-30) REVERT: N 736 GLN cc_start: 0.8296 (tt0) cc_final: 0.8016 (tt0) REVERT: N 745 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6624 (tm-30) outliers start: 199 outliers final: 113 residues processed: 1035 average time/residue: 0.6448 time to fit residues: 820.7156 Evaluate side-chains 1063 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 926 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 532 ARG Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 745 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 348 LYS Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 568 MET Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 666 ASP Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 710 THR Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 236 SER Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 15 ASP Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 501 ILE Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 560 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 675 LYS Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 710 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 270 LYS Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 344 LYS Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 461 THR Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 593 VAL Chi-restraints excluded: chain N residue 660 LEU Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 740 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 207 optimal weight: 0.4980 chunk 249 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 chunk 283 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN B 65 ASN B 433 ASN B 528 ASN B 558 ASN B 703 ASN E 185 GLN F 33 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 736 GLN I 146 ASN I 232 ASN J 52 ASN M 284 ASN N 379 ASN N 413 ASN N 433 ASN N 558 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.156540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119095 restraints weight = 53731.287| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.77 r_work: 0.3312 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39068 Z= 0.137 Angle : 0.549 9.305 54132 Z= 0.315 Chirality : 0.042 0.259 6284 Planarity : 0.004 0.045 5620 Dihedral : 19.315 159.996 8720 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.83 % Allowed : 29.58 % Favored : 65.59 % 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: 1.09 (0.14), residues: 3688 helix: 1.80 (0.12), residues: 1904 sheet: 0.79 (0.22), residues: 576 loop : -1.07 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 718 TYR 0.029 0.002 TYR A 150 PHE 0.027 0.001 PHE M 339 TRP 0.012 0.002 TRP B 697 HIS 0.009 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (39068) covalent geometry : angle 0.54913 / 0.31 (54132) hydrogen bonds : bond 0.04905 / 3.22 ( 1772) hydrogen bonds : angle 4.03793 / 2.85 ( 4928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 924 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8276 (mtmt) REVERT: A 109 SER cc_start: 0.8304 (p) cc_final: 0.8046 (t) REVERT: A 181 ASP cc_start: 0.8356 (m-30) cc_final: 0.7841 (m-30) REVERT: A 284 ASN cc_start: 0.8258 (m110) cc_final: 0.8047 (t0) REVERT: A 342 GLU cc_start: 0.7936 (tt0) cc_final: 0.7592 (tt0) REVERT: B 143 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7142 (t70) REVERT: B 162 ARG cc_start: 0.7964 (tpp80) cc_final: 0.7646 (tpp80) REVERT: B 375 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: B 440 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7770 (ptmm) REVERT: B 461 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8204 (t) REVERT: B 472 LYS cc_start: 0.8480 (tptt) cc_final: 0.8082 (tppt) REVERT: B 482 ASP cc_start: 0.7598 (m-30) cc_final: 0.7239 (m-30) REVERT: B 484 TYR cc_start: 0.6764 (m-80) cc_final: 0.6509 (t80) REVERT: B 497 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7162 (tt) REVERT: B 558 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7652 (t160) REVERT: B 582 MET cc_start: 0.7098 (mmp) cc_final: 0.6537 (mmp) REVERT: B 641 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 677 LYS cc_start: 0.8649 (tptp) cc_final: 0.7997 (tptp) REVERT: B 681 ASN cc_start: 0.8467 (m-40) cc_final: 0.7963 (m110) REVERT: B 708 LYS cc_start: 0.8445 (tttp) cc_final: 0.8168 (ttpp) REVERT: B 738 SER cc_start: 0.8523 (t) cc_final: 0.8246 (m) REVERT: B 745 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 89 SER cc_start: 0.8394 (t) cc_final: 0.8107 (m) REVERT: E 129 LYS cc_start: 0.7153 (pttt) cc_final: 0.6449 (mtmt) REVERT: E 335 SER cc_start: 0.8714 (t) cc_final: 0.8332 (p) REVERT: E 336 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8191 (mp) REVERT: F 78 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7086 (tmt-80) REVERT: F 276 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: F 385 GLU cc_start: 0.8302 (mp0) cc_final: 0.7862 (mp0) REVERT: F 464 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: F 477 LEU cc_start: 0.8550 (mp) cc_final: 0.8338 (mt) REVERT: F 497 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7055 (tt) REVERT: F 509 MET cc_start: 0.8029 (ptp) cc_final: 0.7726 (ptp) REVERT: F 510 ASP cc_start: 0.8703 (m-30) cc_final: 0.8206 (m-30) REVERT: F 525 SER cc_start: 0.8197 (t) cc_final: 0.7879 (p) REVERT: F 556 PHE cc_start: 0.8661 (t80) cc_final: 0.8199 (t80) REVERT: F 558 ASN cc_start: 0.8396 (m-40) cc_final: 0.7844 (m110) REVERT: F 562 ASP cc_start: 0.7207 (m-30) cc_final: 0.6738 (m-30) REVERT: F 582 MET cc_start: 0.7502 (mmp) cc_final: 0.7193 (mmp) REVERT: F 624 PHE cc_start: 0.8264 (t80) cc_final: 0.8001 (t80) REVERT: F 629 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8256 (tppt) REVERT: F 677 LYS cc_start: 0.9004 (tppp) cc_final: 0.8709 (ttmm) REVERT: F 682 ASN cc_start: 0.8109 (m-40) cc_final: 0.7863 (m-40) REVERT: F 723 LEU cc_start: 0.8673 (mm) cc_final: 0.8395 (mt) REVERT: I 39 LYS cc_start: 0.8320 (tttt) cc_final: 0.8117 (pttt) REVERT: I 65 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7839 (mm) REVERT: I 67 LEU cc_start: 0.7942 (mt) cc_final: 0.7574 (mp) REVERT: I 139 LYS cc_start: 0.5594 (tmtt) cc_final: 0.4529 (mmpt) REVERT: I 269 SER cc_start: 0.8388 (m) cc_final: 0.8130 (t) REVERT: I 360 ASP cc_start: 0.7793 (t0) cc_final: 0.7527 (t0) REVERT: J 54 LYS cc_start: 0.8589 (mttt) cc_final: 0.8292 (mmtt) REVERT: J 55 VAL cc_start: 0.8825 (p) cc_final: 0.8591 (m) REVERT: J 97 TYR cc_start: 0.8161 (t80) cc_final: 0.7839 (t80) REVERT: J 344 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8393 (mtmt) REVERT: J 413 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8179 (t160) REVERT: J 472 LYS cc_start: 0.8545 (tttt) cc_final: 0.8263 (ttmm) REVERT: J 494 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7288 (mm-30) REVERT: J 529 LYS cc_start: 0.8268 (ttmm) cc_final: 0.8001 (ttmm) REVERT: J 532 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7952 (ttm-80) REVERT: J 562 ASP cc_start: 0.6724 (m-30) cc_final: 0.6348 (m-30) REVERT: J 568 MET cc_start: 0.5048 (OUTLIER) cc_final: 0.4084 (mmp) REVERT: J 597 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8098 (ttpp) REVERT: J 629 LYS cc_start: 0.8177 (pttt) cc_final: 0.7885 (pttp) REVERT: J 631 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7687 (ttmm) REVERT: J 635 ASP cc_start: 0.6565 (p0) cc_final: 0.6362 (p0) REVERT: J 639 GLU cc_start: 0.6753 (tt0) cc_final: 0.6549 (tt0) REVERT: J 681 ASN cc_start: 0.8090 (t0) cc_final: 0.7883 (m-40) REVERT: M 91 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8605 (mt) REVERT: M 117 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: M 160 MET cc_start: 0.7205 (tpp) cc_final: 0.6899 (tpp) REVERT: M 181 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: M 227 SER cc_start: 0.8485 (p) cc_final: 0.8237 (m) REVERT: M 269 SER cc_start: 0.8602 (m) cc_final: 0.8279 (t) REVERT: M 276 LYS cc_start: 0.8440 (mttp) cc_final: 0.8190 (mttm) REVERT: M 344 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7963 (mmmm) REVERT: N 18 ILE cc_start: 0.8701 (tt) cc_final: 0.8404 (pt) REVERT: N 286 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: N 302 ASN cc_start: 0.8012 (m-40) cc_final: 0.7739 (m-40) REVERT: N 308 SER cc_start: 0.8612 (m) cc_final: 0.8334 (t) REVERT: N 482 ASP cc_start: 0.7532 (m-30) cc_final: 0.7237 (m-30) REVERT: N 494 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7282 (mm-30) REVERT: N 502 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7188 (tp-100) REVERT: N 526 ARG cc_start: 0.8769 (ptm-80) cc_final: 0.8473 (ptm-80) REVERT: N 532 ARG cc_start: 0.8017 (tpp80) cc_final: 0.7680 (tpp80) REVERT: N 534 LEU cc_start: 0.8947 (mt) cc_final: 0.8706 (mp) REVERT: N 547 LEU cc_start: 0.8711 (mt) cc_final: 0.8487 (mt) REVERT: N 550 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7414 (mt-10) REVERT: N 558 ASN cc_start: 0.7916 (m110) cc_final: 0.7656 (m-40) REVERT: N 582 MET cc_start: 0.6747 (mmp) cc_final: 0.6490 (mmp) REVERT: N 639 GLU cc_start: 0.6872 (tt0) cc_final: 0.6348 (tt0) REVERT: N 640 LYS cc_start: 0.8051 (ptmt) cc_final: 0.7741 (ptmt) REVERT: N 656 THR cc_start: 0.8790 (m) cc_final: 0.8526 (p) REVERT: N 679 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: N 708 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7691 (mtpt) REVERT: N 735 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7797 (mm-30) REVERT: N 736 GLN cc_start: 0.8286 (tt0) cc_final: 0.7984 (tt0) REVERT: N 745 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6606 (tm-30) outliers start: 169 outliers final: 92 residues processed: 998 average time/residue: 0.6776 time to fit residues: 827.6276 Evaluate side-chains 1020 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 907 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 745 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 683 GLU Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 548 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 588 ILE Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 672 PHE Chi-restraints excluded: chain J residue 686 PHE Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 707 GLU Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 241 ARG Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 631 LYS Chi-restraints excluded: chain N residue 648 LEU Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 287 optimal weight: 0.2980 chunk 197 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 185 GLN B 65 ASN B 413 ASN B 433 ASN B 508 HIS B 528 ASN B 551 GLN E 185 GLN F 33 ASN F 502 GLN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN I 232 ASN J 52 ASN J 558 ASN M 284 ASN N 379 ASN N 413 ASN N 433 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.154498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.116961 restraints weight = 53606.381| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.75 r_work: 0.3285 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 39068 Z= 0.225 Angle : 0.606 8.583 54132 Z= 0.345 Chirality : 0.045 0.256 6284 Planarity : 0.005 0.044 5620 Dihedral : 19.333 161.402 8720 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.49 % Allowed : 29.72 % Favored : 64.79 % 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: 0.90 (0.14), residues: 3688 helix: 1.66 (0.12), residues: 1904 sheet: 0.46 (0.21), residues: 616 loop : -1.11 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 718 TYR 0.037 0.002 TYR A 150 PHE 0.030 0.002 PHE M 339 TRP 0.014 0.003 TRP B 697 HIS 0.009 0.002 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (39068) covalent geometry : angle 0.60642 / 0.34 (54132) hydrogen bonds : bond 0.05719 / 3.77 ( 1772) hydrogen bonds : angle 4.16626 / 2.94 ( 4928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 932 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6554 (p0) REVERT: A 109 SER cc_start: 0.8303 (p) cc_final: 0.8055 (t) REVERT: A 181 ASP cc_start: 0.8369 (m-30) cc_final: 0.7856 (m-30) REVERT: B 93 HIS cc_start: 0.8426 (m90) cc_final: 0.8139 (m90) REVERT: B 143 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7188 (t70) REVERT: B 162 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7750 (tpp80) REVERT: B 375 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: B 440 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7880 (ptmm) REVERT: B 472 LYS cc_start: 0.8506 (tptt) cc_final: 0.8206 (tppt) REVERT: B 482 ASP cc_start: 0.7603 (m-30) cc_final: 0.7241 (m-30) REVERT: B 484 TYR cc_start: 0.6721 (m-80) cc_final: 0.6490 (t80) REVERT: B 497 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7142 (tt) REVERT: B 558 ASN cc_start: 0.8220 (m-40) cc_final: 0.7964 (m-40) REVERT: B 582 MET cc_start: 0.7109 (mmp) cc_final: 0.6557 (mmp) REVERT: B 677 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8109 (tptp) REVERT: B 681 ASN cc_start: 0.8482 (m-40) cc_final: 0.7967 (m110) REVERT: B 704 TYR cc_start: 0.7807 (t80) cc_final: 0.7498 (t80) REVERT: B 708 LYS cc_start: 0.8507 (tttp) cc_final: 0.8086 (ttmm) REVERT: B 738 SER cc_start: 0.8544 (t) cc_final: 0.8266 (m) REVERT: B 745 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: E 89 SER cc_start: 0.8419 (t) cc_final: 0.8127 (m) REVERT: E 129 LYS cc_start: 0.7208 (pttt) cc_final: 0.6737 (mttt) REVERT: E 167 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: E 296 LYS cc_start: 0.7844 (mmmm) cc_final: 0.7565 (mmmm) REVERT: E 335 SER cc_start: 0.8697 (t) cc_final: 0.8308 (p) REVERT: E 336 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8215 (mp) REVERT: F 78 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7155 (tmt-80) REVERT: F 276 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: F 385 GLU cc_start: 0.8315 (mp0) cc_final: 0.7880 (mp0) REVERT: F 477 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (mt) REVERT: F 509 MET cc_start: 0.8043 (ptp) cc_final: 0.7677 (ptp) REVERT: F 510 ASP cc_start: 0.8750 (m-30) cc_final: 0.8221 (m-30) REVERT: F 525 SER cc_start: 0.8249 (t) cc_final: 0.7925 (p) REVERT: F 556 PHE cc_start: 0.8710 (t80) cc_final: 0.8277 (t80) REVERT: F 558 ASN cc_start: 0.8425 (m-40) cc_final: 0.7874 (m110) REVERT: F 562 ASP cc_start: 0.7263 (m-30) cc_final: 0.6781 (m-30) REVERT: F 582 MET cc_start: 0.7559 (mmp) cc_final: 0.7242 (mmp) REVERT: F 624 PHE cc_start: 0.8301 (t80) cc_final: 0.7972 (t80) REVERT: F 629 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8335 (tppt) REVERT: F 650 PHE cc_start: 0.8688 (m-80) cc_final: 0.8453 (m-80) REVERT: F 677 LYS cc_start: 0.9018 (tppp) cc_final: 0.8729 (ttmm) REVERT: F 723 LEU cc_start: 0.8639 (mm) cc_final: 0.8356 (mt) REVERT: I 39 LYS cc_start: 0.8328 (tttt) cc_final: 0.8112 (pttt) REVERT: I 65 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7865 (mm) REVERT: I 67 LEU cc_start: 0.7934 (mt) cc_final: 0.7574 (mp) REVERT: I 139 LYS cc_start: 0.5666 (tmtt) cc_final: 0.4561 (mmpt) REVERT: I 219 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7924 (mt) REVERT: I 269 SER cc_start: 0.8439 (m) cc_final: 0.8196 (t) REVERT: I 360 ASP cc_start: 0.7822 (t0) cc_final: 0.7574 (t0) REVERT: J 54 LYS cc_start: 0.8585 (mttt) cc_final: 0.8278 (mmtt) REVERT: J 55 VAL cc_start: 0.8840 (p) cc_final: 0.8613 (m) REVERT: J 97 TYR cc_start: 0.8236 (t80) cc_final: 0.7944 (t80) REVERT: J 344 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8439 (mtpp) REVERT: J 413 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8207 (t160) REVERT: J 472 LYS cc_start: 0.8568 (tttt) cc_final: 0.8287 (ttmm) REVERT: J 494 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7240 (mm-30) REVERT: J 529 LYS cc_start: 0.8292 (ttmm) cc_final: 0.8004 (ttmm) REVERT: J 532 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7972 (ttm-80) REVERT: J 568 MET cc_start: 0.5095 (OUTLIER) cc_final: 0.3935 (mmp) REVERT: J 597 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8103 (ttpp) REVERT: J 626 ASN cc_start: 0.8212 (m-40) cc_final: 0.7904 (m110) REVERT: J 631 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7693 (ttmm) REVERT: J 639 GLU cc_start: 0.6740 (tt0) cc_final: 0.6524 (tt0) REVERT: J 641 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7368 (mt-10) REVERT: J 670 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7626 (tp30) REVERT: J 674 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7388 (mm-30) REVERT: J 688 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7615 (tm-30) REVERT: M 91 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (mt) REVERT: M 117 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: M 160 MET cc_start: 0.7171 (tpp) cc_final: 0.6823 (tpp) REVERT: M 181 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: M 211 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8107 (mmmm) REVERT: M 227 SER cc_start: 0.8514 (p) cc_final: 0.8277 (m) REVERT: M 241 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7791 (mtm180) REVERT: M 269 SER cc_start: 0.8604 (m) cc_final: 0.8287 (t) REVERT: M 276 LYS cc_start: 0.8468 (mttp) cc_final: 0.8219 (mttm) REVERT: M 337 VAL cc_start: 0.8523 (t) cc_final: 0.8172 (m) REVERT: M 344 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7976 (mmmm) REVERT: N 18 ILE cc_start: 0.8702 (tt) cc_final: 0.8441 (pt) REVERT: N 286 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: N 302 ASN cc_start: 0.8030 (m-40) cc_final: 0.7783 (m-40) REVERT: N 341 GLN cc_start: 0.8626 (tp40) cc_final: 0.8422 (mm110) REVERT: N 376 ARG cc_start: 0.8408 (ttt90) cc_final: 0.8161 (ttt90) REVERT: N 482 ASP cc_start: 0.7521 (m-30) cc_final: 0.7189 (m-30) REVERT: N 494 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7290 (mm-30) REVERT: N 502 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7250 (tp-100) REVERT: N 532 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7597 (tpp80) REVERT: N 534 LEU cc_start: 0.8945 (mt) cc_final: 0.8701 (mp) REVERT: N 547 LEU cc_start: 0.8689 (mt) cc_final: 0.8480 (mt) REVERT: N 550 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7434 (mt-10) REVERT: N 558 ASN cc_start: 0.7988 (m110) cc_final: 0.7673 (m-40) REVERT: N 582 MET cc_start: 0.6685 (mmp) cc_final: 0.6408 (mmp) REVERT: N 585 ARG cc_start: 0.7214 (ttp80) cc_final: 0.6824 (ptp90) REVERT: N 639 GLU cc_start: 0.6837 (tt0) cc_final: 0.6152 (tt0) REVERT: N 640 LYS cc_start: 0.8047 (ptmt) cc_final: 0.7777 (ptmt) REVERT: N 642 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (tp) REVERT: N 656 THR cc_start: 0.8829 (m) cc_final: 0.8549 (p) REVERT: N 679 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7899 (m-10) REVERT: N 735 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7720 (mm-30) REVERT: N 736 GLN cc_start: 0.8325 (tt0) cc_final: 0.8021 (tt0) REVERT: N 745 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6639 (tm-30) outliers start: 192 outliers final: 118 residues processed: 1016 average time/residue: 0.6712 time to fit residues: 837.4696 Evaluate side-chains 1055 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 913 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 672 PHE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 745 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 457 TYR Chi-restraints excluded: chain F residue 458 SER Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 275 LEU Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 560 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 588 ILE Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 672 PHE Chi-restraints excluded: chain J residue 686 PHE Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 719 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 241 ARG Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain N residue 348 LYS Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 403 LEU Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 593 VAL Chi-restraints excluded: chain N residue 642 ILE Chi-restraints excluded: chain N residue 648 LEU Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 740 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 379 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 382 optimal weight: 0.5980 chunk 380 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 433 ASN B 528 ASN B 703 ASN E 185 GLN F 33 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 558 ASN M 284 ASN M 364 HIS N 379 ASN N 413 ASN N 433 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.155351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117980 restraints weight = 53574.797| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.76 r_work: 0.3302 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39068 Z= 0.162 Angle : 0.574 8.865 54132 Z= 0.326 Chirality : 0.043 0.255 6284 Planarity : 0.004 0.044 5620 Dihedral : 19.336 161.614 8720 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.18 % Allowed : 30.38 % Favored : 64.45 % 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 (0.14), residues: 3688 helix: 1.74 (0.12), residues: 1900 sheet: 0.47 (0.21), residues: 616 loop : -1.08 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 718 TYR 0.033 0.002 TYR A 150 PHE 0.032 0.001 PHE M 339 TRP 0.014 0.002 TRP J 139 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (39068) covalent geometry : angle 0.57394 / 0.33 (54132) hydrogen bonds : bond 0.05105 / 3.37 ( 1772) hydrogen bonds : angle 4.09915 / 2.90 ( 4928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 912 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6605 (p0) REVERT: A 109 SER cc_start: 0.8292 (p) cc_final: 0.8044 (t) REVERT: A 181 ASP cc_start: 0.8354 (m-30) cc_final: 0.7826 (m-30) REVERT: A 342 GLU cc_start: 0.7880 (tt0) cc_final: 0.7523 (tt0) REVERT: B 93 HIS cc_start: 0.8415 (m90) cc_final: 0.8151 (m90) REVERT: B 143 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7161 (t70) REVERT: B 162 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7723 (tpp80) REVERT: B 375 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: B 440 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7839 (ptmm) REVERT: B 472 LYS cc_start: 0.8477 (tptt) cc_final: 0.8181 (tppt) REVERT: B 482 ASP cc_start: 0.7594 (m-30) cc_final: 0.7226 (m-30) REVERT: B 484 TYR cc_start: 0.6727 (m-80) cc_final: 0.6499 (t80) REVERT: B 497 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 582 MET cc_start: 0.7042 (mmp) cc_final: 0.6493 (mmp) REVERT: B 677 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8077 (tptp) REVERT: B 681 ASN cc_start: 0.8467 (m-40) cc_final: 0.7942 (m110) REVERT: B 704 TYR cc_start: 0.7763 (t80) cc_final: 0.7421 (t80) REVERT: B 708 LYS cc_start: 0.8495 (tttp) cc_final: 0.8055 (ttmm) REVERT: B 718 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7737 (mtt90) REVERT: B 738 SER cc_start: 0.8541 (t) cc_final: 0.8264 (m) REVERT: B 745 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: E 89 SER cc_start: 0.8404 (t) cc_final: 0.8123 (m) REVERT: E 129 LYS cc_start: 0.7179 (pttt) cc_final: 0.6689 (mttt) REVERT: E 296 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7560 (mmmm) REVERT: E 335 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8304 (p) REVERT: E 336 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8191 (mp) REVERT: F 78 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7099 (tmt-80) REVERT: F 276 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: F 385 GLU cc_start: 0.8301 (mp0) cc_final: 0.7855 (mp0) REVERT: F 477 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (mt) REVERT: F 509 MET cc_start: 0.8029 (ptp) cc_final: 0.7670 (ptp) REVERT: F 510 ASP cc_start: 0.8758 (m-30) cc_final: 0.8270 (m-30) REVERT: F 525 SER cc_start: 0.8197 (t) cc_final: 0.7878 (p) REVERT: F 556 PHE cc_start: 0.8690 (t80) cc_final: 0.8235 (t80) REVERT: F 562 ASP cc_start: 0.7300 (m-30) cc_final: 0.6782 (m-30) REVERT: F 582 MET cc_start: 0.7530 (mmp) cc_final: 0.7204 (mmp) REVERT: F 624 PHE cc_start: 0.8265 (t80) cc_final: 0.7956 (t80) REVERT: F 629 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8260 (tppt) REVERT: F 650 PHE cc_start: 0.8687 (m-80) cc_final: 0.8442 (m-80) REVERT: F 677 LYS cc_start: 0.9004 (tppp) cc_final: 0.8716 (ttmm) REVERT: F 682 ASN cc_start: 0.8118 (m-40) cc_final: 0.7876 (m-40) REVERT: F 723 LEU cc_start: 0.8602 (mm) cc_final: 0.8291 (mt) REVERT: I 39 LYS cc_start: 0.8301 (tttt) cc_final: 0.8087 (pttt) REVERT: I 65 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7864 (mm) REVERT: I 67 LEU cc_start: 0.7947 (mt) cc_final: 0.7572 (mp) REVERT: I 139 LYS cc_start: 0.5550 (tmtt) cc_final: 0.4476 (mmpt) REVERT: I 269 SER cc_start: 0.8428 (m) cc_final: 0.8189 (t) REVERT: I 360 ASP cc_start: 0.7744 (t0) cc_final: 0.7504 (t0) REVERT: J 54 LYS cc_start: 0.8579 (mttt) cc_final: 0.8288 (mmtt) REVERT: J 55 VAL cc_start: 0.8837 (p) cc_final: 0.8605 (m) REVERT: J 97 TYR cc_start: 0.8193 (t80) cc_final: 0.7866 (t80) REVERT: J 344 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8484 (mtmt) REVERT: J 413 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8206 (t160) REVERT: J 435 ASN cc_start: 0.7849 (p0) cc_final: 0.7556 (p0) REVERT: J 472 LYS cc_start: 0.8546 (tttt) cc_final: 0.8262 (ttmm) REVERT: J 494 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7307 (mm-30) REVERT: J 529 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7995 (ttmm) REVERT: J 532 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7976 (ttm-80) REVERT: J 568 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.3980 (mmp) REVERT: J 597 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8090 (ttpp) REVERT: J 641 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7216 (mt-10) REVERT: J 688 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7589 (tm-30) REVERT: M 91 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (mt) REVERT: M 117 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: M 160 MET cc_start: 0.7199 (tpp) cc_final: 0.6857 (tpp) REVERT: M 180 MET cc_start: 0.8343 (mmm) cc_final: 0.8087 (tpp) REVERT: M 181 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7857 (m-30) REVERT: M 211 LYS cc_start: 0.8280 (mmmm) cc_final: 0.8069 (mmmm) REVERT: M 227 SER cc_start: 0.8481 (p) cc_final: 0.8240 (m) REVERT: M 241 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7744 (mtm180) REVERT: M 269 SER cc_start: 0.8581 (m) cc_final: 0.8255 (t) REVERT: M 276 LYS cc_start: 0.8449 (mttp) cc_final: 0.8202 (mttm) REVERT: M 337 VAL cc_start: 0.8507 (t) cc_final: 0.8146 (m) REVERT: M 344 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7963 (mmmm) REVERT: N 18 ILE cc_start: 0.8681 (tt) cc_final: 0.8416 (pt) REVERT: N 286 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7300 (mm-30) REVERT: N 302 ASN cc_start: 0.8014 (m-40) cc_final: 0.7745 (m-40) REVERT: N 373 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8389 (m) REVERT: N 376 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8101 (ttt90) REVERT: N 482 ASP cc_start: 0.7481 (m-30) cc_final: 0.7148 (m-30) REVERT: N 494 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7293 (mm-30) REVERT: N 502 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7259 (tp-100) REVERT: N 532 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7600 (tpp80) REVERT: N 534 LEU cc_start: 0.8942 (mt) cc_final: 0.8702 (mp) REVERT: N 550 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7073 (mt-10) REVERT: N 582 MET cc_start: 0.6775 (mmp) cc_final: 0.6563 (mmp) REVERT: N 631 LYS cc_start: 0.8540 (tttm) cc_final: 0.7996 (tptp) REVERT: N 639 GLU cc_start: 0.6773 (tt0) cc_final: 0.5996 (tt0) REVERT: N 640 LYS cc_start: 0.8050 (ptmt) cc_final: 0.7723 (mppt) REVERT: N 642 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7874 (tp) REVERT: N 656 THR cc_start: 0.8756 (m) cc_final: 0.8488 (p) REVERT: N 679 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7823 (m-10) REVERT: N 735 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7707 (mm-30) REVERT: N 736 GLN cc_start: 0.8320 (tt0) cc_final: 0.8011 (tt0) REVERT: N 745 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6614 (tm-30) outliers start: 181 outliers final: 114 residues processed: 994 average time/residue: 0.6756 time to fit residues: 824.8204 Evaluate side-chains 1051 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 913 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 672 PHE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 745 GLU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 457 TYR Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 633 TYR Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 706 ILE Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 560 ILE Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 588 ILE Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 635 ASP Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 672 PHE Chi-restraints excluded: chain J residue 686 PHE Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 724 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 241 ARG Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 286 GLU Chi-restraints excluded: chain N residue 289 VAL Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 403 LEU Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 593 VAL Chi-restraints excluded: chain N residue 642 ILE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 86 optimal weight: 2.9990 chunk 397 optimal weight: 9.9990 chunk 344 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 345 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 354 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 282 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 433 ASN B 528 ASN B 551 GLN B 591 GLN E 185 GLN E 353 GLN F 33 ASN F 502 GLN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN J 52 ASN J 88 ASN J 558 ASN M 284 ASN M 364 HIS N 379 ASN N 413 ASN N 433 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118814 restraints weight = 54239.645| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.76 r_work: 0.3313 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 39068 Z= 0.140 Angle : 0.564 9.226 54132 Z= 0.320 Chirality : 0.042 0.264 6284 Planarity : 0.004 0.057 5620 Dihedral : 19.308 161.442 8720 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.35 % Allowed : 31.41 % Favored : 64.24 % 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: 1.05 (0.14), residues: 3688 helix: 1.81 (0.12), residues: 1900 sheet: 0.52 (0.21), residues: 616 loop : -1.06 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 664 TYR 0.032 0.002 TYR A 150 PHE 0.031 0.001 PHE M 339 TRP 0.012 0.002 TRP J 139 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (39068) covalent geometry : angle 0.56361 / 0.32 (54132) hydrogen bonds : bond 0.04696 / 3.10 ( 1772) hydrogen bonds : angle 4.06816 / 2.87 ( 4928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 901 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6640 (p0) REVERT: A 109 SER cc_start: 0.8274 (p) cc_final: 0.8007 (t) REVERT: A 181 ASP cc_start: 0.8363 (m-30) cc_final: 0.7857 (m-30) REVERT: A 342 GLU cc_start: 0.7831 (tt0) cc_final: 0.7500 (tt0) REVERT: B 93 HIS cc_start: 0.8417 (m90) cc_final: 0.8178 (m90) REVERT: B 162 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7695 (tpp80) REVERT: B 375 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: B 440 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7821 (ptmm) REVERT: B 461 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8467 (t) REVERT: B 472 LYS cc_start: 0.8484 (tptt) cc_final: 0.8194 (tppt) REVERT: B 482 ASP cc_start: 0.7546 (m-30) cc_final: 0.7202 (m-30) REVERT: B 484 TYR cc_start: 0.6746 (m-80) cc_final: 0.6522 (t80) REVERT: B 497 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7197 (tt) REVERT: B 582 MET cc_start: 0.7057 (mmp) cc_final: 0.6531 (mmp) REVERT: B 677 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8091 (tptp) REVERT: B 681 ASN cc_start: 0.8431 (m-40) cc_final: 0.7931 (m110) REVERT: B 704 TYR cc_start: 0.7698 (t80) cc_final: 0.7333 (t80) REVERT: B 708 LYS cc_start: 0.8508 (tttp) cc_final: 0.8043 (ttmm) REVERT: B 738 SER cc_start: 0.8472 (t) cc_final: 0.8203 (m) REVERT: B 745 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7144 (tm-30) REVERT: E 89 SER cc_start: 0.8412 (t) cc_final: 0.8161 (m) REVERT: E 296 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7559 (mmmm) REVERT: E 335 SER cc_start: 0.8713 (t) cc_final: 0.8333 (p) REVERT: E 336 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8149 (mp) REVERT: F 276 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: F 307 TYR cc_start: 0.8322 (t80) cc_final: 0.8099 (t80) REVERT: F 385 GLU cc_start: 0.8280 (mp0) cc_final: 0.7840 (mp0) REVERT: F 509 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7537 (ptp) REVERT: F 510 ASP cc_start: 0.8759 (m-30) cc_final: 0.8218 (m-30) REVERT: F 525 SER cc_start: 0.8166 (t) cc_final: 0.7844 (p) REVERT: F 556 PHE cc_start: 0.8683 (t80) cc_final: 0.8237 (t80) REVERT: F 558 ASN cc_start: 0.8377 (m-40) cc_final: 0.7822 (m110) REVERT: F 562 ASP cc_start: 0.7324 (m-30) cc_final: 0.6795 (m-30) REVERT: F 582 MET cc_start: 0.7458 (mmp) cc_final: 0.7136 (mmp) REVERT: F 624 PHE cc_start: 0.8254 (t80) cc_final: 0.7981 (t80) REVERT: F 629 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8274 (tppt) REVERT: F 677 LYS cc_start: 0.8991 (tppp) cc_final: 0.8702 (ttmm) REVERT: F 682 ASN cc_start: 0.8121 (m-40) cc_final: 0.7878 (m-40) REVERT: F 704 TYR cc_start: 0.8221 (t80) cc_final: 0.7956 (t80) REVERT: F 723 LEU cc_start: 0.8609 (mm) cc_final: 0.8301 (mt) REVERT: I 65 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7840 (mm) REVERT: I 67 LEU cc_start: 0.7927 (mt) cc_final: 0.7575 (mp) REVERT: I 139 LYS cc_start: 0.5582 (tmtt) cc_final: 0.4483 (mmpt) REVERT: I 269 SER cc_start: 0.8400 (m) cc_final: 0.8162 (t) REVERT: I 360 ASP cc_start: 0.7753 (t0) cc_final: 0.7509 (t0) REVERT: J 54 LYS cc_start: 0.8582 (mttt) cc_final: 0.8287 (mmtt) REVERT: J 55 VAL cc_start: 0.8824 (p) cc_final: 0.8593 (m) REVERT: J 97 TYR cc_start: 0.8143 (t80) cc_final: 0.7850 (t80) REVERT: J 344 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8401 (mtmt) REVERT: J 413 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8232 (t160) REVERT: J 435 ASN cc_start: 0.7805 (p0) cc_final: 0.7491 (p0) REVERT: J 472 LYS cc_start: 0.8546 (tttt) cc_final: 0.8261 (ttmm) REVERT: J 494 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7268 (mm-30) REVERT: J 529 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7997 (ttmm) REVERT: J 568 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.3968 (mmp) REVERT: J 597 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8083 (ttpp) REVERT: J 629 LYS cc_start: 0.8279 (ptpp) cc_final: 0.8042 (pmtt) REVERT: J 631 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7665 (ttmm) REVERT: J 641 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7263 (mt-10) REVERT: J 674 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7972 (tp30) REVERT: J 688 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7583 (tm-30) REVERT: M 91 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (mt) REVERT: M 117 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: M 160 MET cc_start: 0.7214 (tpp) cc_final: 0.6858 (tpp) REVERT: M 181 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: M 211 LYS cc_start: 0.8233 (mmmm) cc_final: 0.8026 (mmmm) REVERT: M 227 SER cc_start: 0.8476 (p) cc_final: 0.8227 (m) REVERT: M 241 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7672 (mtm180) REVERT: M 269 SER cc_start: 0.8540 (m) cc_final: 0.8217 (t) REVERT: M 276 LYS cc_start: 0.8436 (mttp) cc_final: 0.8190 (mttm) REVERT: M 344 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7876 (mmmm) REVERT: N 18 ILE cc_start: 0.8643 (tt) cc_final: 0.8413 (pt) REVERT: N 286 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7320 (mm-30) REVERT: N 302 ASN cc_start: 0.7979 (m-40) cc_final: 0.7701 (m-40) REVERT: N 306 ILE cc_start: 0.8668 (mt) cc_final: 0.8333 (tt) REVERT: N 373 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8385 (m) REVERT: N 376 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8089 (ttt90) REVERT: N 414 LEU cc_start: 0.8370 (mt) cc_final: 0.8169 (mp) REVERT: N 458 SER cc_start: 0.8331 (m) cc_final: 0.7969 (t) REVERT: N 482 ASP cc_start: 0.7408 (m-30) cc_final: 0.7083 (m-30) REVERT: N 494 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7276 (mm-30) REVERT: N 502 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7253 (tp-100) REVERT: N 526 ARG cc_start: 0.8749 (ptm-80) cc_final: 0.8511 (ptm-80) REVERT: N 532 ARG cc_start: 0.7998 (tpp80) cc_final: 0.7590 (tpp80) REVERT: N 534 LEU cc_start: 0.8941 (mt) cc_final: 0.8694 (mp) REVERT: N 558 ASN cc_start: 0.7970 (m110) cc_final: 0.7743 (m-40) REVERT: N 560 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8820 (mm) REVERT: N 582 MET cc_start: 0.6720 (mmp) cc_final: 0.6487 (mmp) REVERT: N 585 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6701 (pmm-80) REVERT: N 631 LYS cc_start: 0.8521 (tttm) cc_final: 0.7975 (tptp) REVERT: N 640 LYS cc_start: 0.7999 (ptmt) cc_final: 0.7729 (ptmt) REVERT: N 642 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7844 (tp) REVERT: N 656 THR cc_start: 0.8725 (m) cc_final: 0.8451 (p) REVERT: N 679 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7798 (m-10) REVERT: N 735 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7821 (mm-30) REVERT: N 736 GLN cc_start: 0.8323 (tt0) cc_final: 0.8010 (tt0) REVERT: N 745 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6638 (tm-30) outliers start: 152 outliers final: 89 residues processed: 967 average time/residue: 0.6879 time to fit residues: 814.0687 Evaluate side-chains 1005 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 895 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 633 TYR Chi-restraints excluded: chain B residue 672 PHE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 457 TYR Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 588 ILE Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 672 PHE Chi-restraints excluded: chain J residue 686 PHE Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 724 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 241 ARG Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 341 SER Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain N residue 373 SER Chi-restraints excluded: chain N residue 375 GLU Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 560 ILE Chi-restraints excluded: chain N residue 593 VAL Chi-restraints excluded: chain N residue 642 ILE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 681 ASN Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 58 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 340 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 329 optimal weight: 0.9980 chunk 288 optimal weight: 0.7980 chunk 396 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 365 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 185 GLN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS B 65 ASN B 433 ASN B 528 ASN ** B 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 ASN J 558 ASN M 284 ASN M 364 HIS N 259 ASN N 379 ASN N 413 ASN N 433 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118833 restraints weight = 53547.062| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.75 r_work: 0.3312 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39068 Z= 0.144 Angle : 0.570 9.433 54132 Z= 0.321 Chirality : 0.042 0.253 6284 Planarity : 0.004 0.055 5620 Dihedral : 19.289 161.493 8720 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.83 % Allowed : 32.04 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.14), residues: 3688 helix: 1.82 (0.12), residues: 1900 sheet: 0.54 (0.21), residues: 616 loop : -1.05 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 718 TYR 0.032 0.002 TYR A 150 PHE 0.032 0.001 PHE M 339 TRP 0.012 0.002 TRP J 139 HIS 0.016 0.001 HIS M 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (39068) covalent geometry : angle 0.57014 / 0.32 (54132) hydrogen bonds : bond 0.04654 / 3.07 ( 1772) hydrogen bonds : angle 4.05063 / 2.86 ( 4928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 903 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6641 (p0) REVERT: A 109 SER cc_start: 0.8273 (p) cc_final: 0.7988 (t) REVERT: A 181 ASP cc_start: 0.8354 (m-30) cc_final: 0.7846 (m-30) REVERT: A 342 GLU cc_start: 0.7813 (tt0) cc_final: 0.7482 (tt0) REVERT: B 93 HIS cc_start: 0.8418 (m90) cc_final: 0.8174 (m90) REVERT: B 162 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7713 (tpp80) REVERT: B 375 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: B 440 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7828 (ptmm) REVERT: B 461 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (t) REVERT: B 472 LYS cc_start: 0.8475 (tptt) cc_final: 0.8184 (tppt) REVERT: B 482 ASP cc_start: 0.7529 (m-30) cc_final: 0.7177 (m-30) REVERT: B 484 TYR cc_start: 0.6712 (m-80) cc_final: 0.6496 (t80) REVERT: B 497 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7189 (tt) REVERT: B 550 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 582 MET cc_start: 0.7019 (mmp) cc_final: 0.6488 (mmp) REVERT: B 677 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8110 (tptp) REVERT: B 681 ASN cc_start: 0.8426 (m-40) cc_final: 0.7926 (m110) REVERT: B 704 TYR cc_start: 0.7687 (t80) cc_final: 0.7315 (t80) REVERT: B 708 LYS cc_start: 0.8497 (tttp) cc_final: 0.8044 (ttmm) REVERT: B 738 SER cc_start: 0.8457 (t) cc_final: 0.8189 (m) REVERT: B 745 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7147 (tm-30) REVERT: E 89 SER cc_start: 0.8404 (t) cc_final: 0.8158 (m) REVERT: E 326 LEU cc_start: 0.8327 (mt) cc_final: 0.8075 (mm) REVERT: E 335 SER cc_start: 0.8716 (t) cc_final: 0.8328 (p) REVERT: E 336 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8131 (mp) REVERT: F 276 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6929 (pt0) REVERT: F 307 TYR cc_start: 0.8305 (t80) cc_final: 0.8076 (t80) REVERT: F 385 GLU cc_start: 0.8287 (mp0) cc_final: 0.7845 (mp0) REVERT: F 464 PHE cc_start: 0.7778 (m-10) cc_final: 0.7470 (m-10) REVERT: F 509 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7520 (ptp) REVERT: F 510 ASP cc_start: 0.8755 (m-30) cc_final: 0.8185 (m-30) REVERT: F 525 SER cc_start: 0.8144 (t) cc_final: 0.7826 (p) REVERT: F 556 PHE cc_start: 0.8681 (t80) cc_final: 0.8189 (t80) REVERT: F 558 ASN cc_start: 0.8372 (m-40) cc_final: 0.7816 (m110) REVERT: F 562 ASP cc_start: 0.7317 (m-30) cc_final: 0.6787 (m-30) REVERT: F 582 MET cc_start: 0.7467 (mmp) cc_final: 0.7142 (mmp) REVERT: F 629 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8275 (tppt) REVERT: F 650 PHE cc_start: 0.8656 (m-80) cc_final: 0.8384 (m-80) REVERT: F 655 GLU cc_start: 0.7732 (tt0) cc_final: 0.7509 (tt0) REVERT: F 677 LYS cc_start: 0.8993 (tppp) cc_final: 0.8705 (ttmm) REVERT: F 682 ASN cc_start: 0.8127 (m-40) cc_final: 0.7879 (m-40) REVERT: F 704 TYR cc_start: 0.8203 (t80) cc_final: 0.7933 (t80) REVERT: F 723 LEU cc_start: 0.8597 (mm) cc_final: 0.8289 (mt) REVERT: I 65 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7832 (mm) REVERT: I 67 LEU cc_start: 0.7944 (mt) cc_final: 0.7558 (mp) REVERT: I 139 LYS cc_start: 0.5668 (tmtt) cc_final: 0.4553 (mmpt) REVERT: I 269 SER cc_start: 0.8400 (m) cc_final: 0.8157 (t) REVERT: I 360 ASP cc_start: 0.7753 (t0) cc_final: 0.7501 (t0) REVERT: J 54 LYS cc_start: 0.8579 (mttt) cc_final: 0.8282 (mmtt) REVERT: J 55 VAL cc_start: 0.8822 (p) cc_final: 0.8585 (m) REVERT: J 97 TYR cc_start: 0.8144 (t80) cc_final: 0.7855 (t80) REVERT: J 344 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: J 413 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8242 (t160) REVERT: J 435 ASN cc_start: 0.7806 (p0) cc_final: 0.7516 (p0) REVERT: J 472 LYS cc_start: 0.8541 (tttt) cc_final: 0.8254 (ttmm) REVERT: J 494 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7199 (mm-30) REVERT: J 529 LYS cc_start: 0.8279 (ttmm) cc_final: 0.8001 (ttmm) REVERT: J 568 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4071 (mmp) REVERT: J 597 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8091 (ttpp) REVERT: J 631 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7872 (ttmm) REVERT: J 641 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7297 (mt-10) REVERT: J 674 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7976 (tp30) REVERT: J 688 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7584 (tm-30) REVERT: M 49 LYS cc_start: 0.8090 (mttt) cc_final: 0.7704 (mmtt) REVERT: M 91 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8588 (mt) REVERT: M 117 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: M 160 MET cc_start: 0.7203 (tpp) cc_final: 0.6855 (tpp) REVERT: M 181 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: M 211 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8041 (mmmm) REVERT: M 227 SER cc_start: 0.8483 (p) cc_final: 0.8229 (m) REVERT: M 241 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7648 (mtm180) REVERT: M 269 SER cc_start: 0.8535 (m) cc_final: 0.8210 (t) REVERT: M 276 LYS cc_start: 0.8445 (mttp) cc_final: 0.8190 (mttm) REVERT: M 337 VAL cc_start: 0.8513 (t) cc_final: 0.8143 (m) REVERT: M 344 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7866 (mmmm) REVERT: N 286 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7303 (mm-30) REVERT: N 302 ASN cc_start: 0.7990 (m-40) cc_final: 0.7723 (m-40) REVERT: N 373 SER cc_start: 0.8590 (p) cc_final: 0.8385 (m) REVERT: N 376 ARG cc_start: 0.8350 (ttt90) cc_final: 0.8079 (ttt90) REVERT: N 458 SER cc_start: 0.8303 (m) cc_final: 0.7950 (t) REVERT: N 482 ASP cc_start: 0.7403 (m-30) cc_final: 0.7085 (m-30) REVERT: N 494 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7282 (mm-30) REVERT: N 502 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7288 (tp-100) REVERT: N 526 ARG cc_start: 0.8724 (ptm-80) cc_final: 0.8508 (ptm-80) REVERT: N 532 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7586 (tpp80) REVERT: N 534 LEU cc_start: 0.8937 (mt) cc_final: 0.8692 (mp) REVERT: N 558 ASN cc_start: 0.7960 (m110) cc_final: 0.7701 (m-40) REVERT: N 582 MET cc_start: 0.6704 (mmp) cc_final: 0.6388 (mmp) REVERT: N 631 LYS cc_start: 0.8520 (tttm) cc_final: 0.8070 (tptp) REVERT: N 639 GLU cc_start: 0.6730 (tt0) cc_final: 0.6342 (tt0) REVERT: N 640 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7718 (ptmt) REVERT: N 642 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7860 (tp) REVERT: N 656 THR cc_start: 0.8722 (m) cc_final: 0.8446 (p) REVERT: N 679 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7835 (m-10) REVERT: N 735 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7805 (mm-30) REVERT: N 736 GLN cc_start: 0.8328 (tt0) cc_final: 0.8016 (tt0) REVERT: N 745 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6650 (tm-30) outliers start: 134 outliers final: 91 residues processed: 963 average time/residue: 0.6920 time to fit residues: 815.4124 Evaluate side-chains 1006 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 896 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 672 PHE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 ASN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 270 LYS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 457 TYR Chi-restraints excluded: chain F residue 497 LEU Chi-restraints excluded: chain F residue 509 MET Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 639 GLU Chi-restraints excluded: chain F residue 670 GLU Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 744 GLU Chi-restraints excluded: chain F residue 747 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 125 SER Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain I residue 239 ILE Chi-restraints excluded: chain I residue 270 LYS Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 279 SER Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 344 LYS Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 413 ASN Chi-restraints excluded: chain J residue 425 ASP Chi-restraints excluded: chain J residue 442 SER Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 544 GLU Chi-restraints excluded: chain J residue 568 MET Chi-restraints excluded: chain J residue 588 ILE Chi-restraints excluded: chain J residue 633 TYR Chi-restraints excluded: chain J residue 660 LEU Chi-restraints excluded: chain J residue 672 PHE Chi-restraints excluded: chain J residue 686 PHE Chi-restraints excluded: chain J residue 702 LEU Chi-restraints excluded: chain J residue 724 SER Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain M residue 117 PHE Chi-restraints excluded: chain M residue 123 SER Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 241 ARG Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 260 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 322 LEU Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 366 GLN Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain N residue 401 THR Chi-restraints excluded: chain N residue 442 SER Chi-restraints excluded: chain N residue 477 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 593 VAL Chi-restraints excluded: chain N residue 642 ILE Chi-restraints excluded: chain N residue 679 TYR Chi-restraints excluded: chain N residue 686 PHE Chi-restraints excluded: chain N residue 687 LEU Chi-restraints excluded: chain N residue 731 ILE Chi-restraints excluded: chain N residue 742 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 53 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 361 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 389 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN ** A 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 433 ASN B 528 ASN B 558 ASN E 185 GLN F 33 ASN F 502 GLN ** F 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 ASN I 353 GLN J 52 ASN J 558 ASN M 284 ASN M 353 GLN M 364 HIS N 379 ASN N 413 ASN N 433 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.118520 restraints weight = 53791.545| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.77 r_work: 0.3305 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39068 Z= 0.155 Angle : 0.580 10.265 54132 Z= 0.327 Chirality : 0.043 0.258 6284 Planarity : 0.004 0.061 5620 Dihedral : 19.279 161.505 8720 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.09 % Allowed : 32.01 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.14), residues: 3688 helix: 1.79 (0.12), residues: 1900 sheet: 0.54 (0.21), residues: 616 loop : -1.06 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 583 TYR 0.039 0.002 TYR A 150 PHE 0.034 0.001 PHE M 339 TRP 0.013 0.002 TRP B 139 HIS 0.015 0.001 HIS M 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (39068) covalent geometry : angle 0.57961 / 0.33 (54132) hydrogen bonds : bond 0.04804 / 3.18 ( 1772) hydrogen bonds : angle 4.07276 / 2.88 ( 4928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18494.03 seconds wall clock time: 314 minutes 57.88 seconds (18897.88 seconds total)